A second-half Peter Leven penalty gave MK Dons a share of the spoils and ended a run of four successive defeats.
Dean Bowditch put Yeovil ahead after just 33 seconds when he raced on to Gavin Tomlin's precise pass and beat keeper Willy Gueret at his near post.
Sam Baldock soon levelled when he drilled in from an acute angle.
MacDonald restored the Glovers' lead in the 17th minute, before Leven coolly converted from the spot after Terrell Forbes fouled Aaron Wilbraham.
MK Dons manager Paul Ince told BBC Three Counties Radio:
"We had the chances to win the game but I am more disappointed with the things that we worked on this week and we threw it away after 34 seconds.
"The defending was diabolical and it happened twice. You are talking about two experienced centre-halves there."
Yeovil manager Terry Skiverton told BBC Somerset:
"Dean Bowditch was clear, one-on-one with the goalkeeper and about to score he gets brought down and the man should be sent off [David McCracken was booked].
"Every time we come to a big place like this we seem to be getting let down by officials.
"As a small club in League One we are being let down by people not brave enough to make decisions."
90:00+4:19 The final whistle is blown by the referee.
90:00+2:21 Corner taken by Jason Puncheon, save by Alex McCarthy. Inswinging corner taken by Martin Devaney, clearance by Craig Alcock.
90:00+0:49 Corner from the left by-line taken by Martin Devaney, Steven Caulker makes a clearance. Inswinging corner taken left-footed by Jason Puncheon.
88:05 Substitution (Milton Keynes Dons) makes a substitution, with Stephen Gleeson coming on for Nigel Quashie.
Correction - 87:08 Inswinging corner taken left-footed by Jason Puncheon played to the near post, clearance by Sam Williams.
87:08 Jason Puncheon takes a inswinging corner to the near post, Sam Williams makes a clearance.
86:23 Free kick awarded for a foul by Shaun MacDonald on Peter Leven. Free kick taken by Willy Gueret.
83:05 Martin Devaney concedes a free kick for a foul on Nathan Smith. George O'Callaghan crosses the ball from the free kick right-footed from left wing, Luke Howell manages to make a clearance.
81:53 Craig Alcock challenges Sam Baldock unfairly and gives away a free kick. Peter Leven takes the direct free kick.
79:33 Inswinging corner taken left-footed by Jason Puncheon, David McCracken takes a shot. Save made by Alex McCarthy.
78:19 Jason Puncheon takes the direct free kick.
78:19 Booking JP Kalala shown a yellow card.
78:04 Unfair challenge on Dean Lewington by JP Kalala results in a free kick.
75:31 Jason Puncheon takes the outswinging corner, save by Alex McCarthy.
73:32 Substitution Martin Devaney joins the action as a substitute, replacing Luke Chadwick.
73:17 Substitution (Milton Keynes Dons) makes a substitution, with Martin Devaney coming on for Luke Chadwick.
72:44 Substitution Dean Bowditch goes off and Jonathan Obika comes on.
71:34 Free kick awarded for a foul by Luke Chadwick on JP Kalala. Alex McCarthy takes the free kick.
66:19 Free kick taken by George O'Callaghan. Effort from the edge of the penalty area by Dean Bowditch goes wide of the left-hand post.
66:19 Booking Booking for Peter Leven for unsporting behaviour.
65:58 Foul by Peter Leven on Shaun MacDonald, free kick awarded.
65:17 GOAL - Peter Leven:MK Dons 2 - 2 Yeovil Peter Leven scores a power penalty. Milton Keynes Dons 2-2 Yeovil.
62:50 Shot by Luke Chadwick. Terrell Forbes gets a block in. Corner taken left-footed by Jason Puncheon, Craig Alcock makes a clearance. Nigel Quashie takes the inswinging corner, Terrell Forbes gives away a Penalty for an unfair challenge on Aaron Wilbraham.
62:38 Dean Lewington sends in a cross, Terrell Forbes manages to make a clearance.
62:11 The assistant referee signals for offside against Dean Bowditch. Willy Gueret takes the indirect free kick.
61:20 Substitution Ryan Mason goes off and George O'Callaghan comes on.
60:48 The ball is sent over by Luke Chadwick, Shaun MacDonald makes a clearance.
59:13 Jason Puncheon takes the outswinging corner, Nigel Quashie takes a shot.
57:11 JP Kalala concedes a free kick for a foul on Luke Chadwick. Free kick taken by Jason Puncheon. Shot by Luke Howell from outside the box goes high over the target.
56:17 Luke Howell delivers the ball, clearance by Terrell Forbes. Peter Leven produces a left-footed shot from just outside the area that goes harmlessly over the target.
55:43 Jason Puncheon takes the free kick.
55:43 Booking Booking for Terrell Forbes for unsporting behaviour.
55:21 Luke Chadwick fouled by Terrell Forbes, the ref awards a free kick.
52:40 Corner taken by Jason Puncheon from the right by-line to the near post, Sam Williams manages to make a clearance. Inswinging corner taken from the right by-line by Jason Puncheon, Aaron Wilbraham produces a header from inside the area that goes over the bar.
51:29 Effort on goal by Luke Chadwick from just inside the area clears the bar.
49:47 Nigel Quashie concedes a free kick for a foul on Sam Williams. Free kick taken by Ryan Mason.
48:17 Ryan Mason restarts play with the free kick.
48:17 Booking Jason Puncheon receives a yellow card for unsporting behaviour.
47:50 Jason Puncheon challenges Nathan Smith unfairly and gives away a free kick.
45:01 The second half kicks off.
Half Time
45:00+2:59 The referee blows for half time.
45:00+0:10 Aaron Wilbraham fouled by Dean Bowditch, the ref awards a free kick. Willy Gueret takes the direct free kick. Free kick awarded for an unfair challenge on Ryan Mason by Dean Lewington. Alex McCarthy restarts play with the free kick.
42:19 Sam Baldock is caught offside. Steven Caulker takes the indirect free kick.
40:55 Free kick awarded for an unfair challenge on Willy Gueret by Sam Williams. Willy Gueret restarts play with the free kick.
40:13 JP Kalala handles the ball and concedes a free kick. Luke Chadwick restarts play with the free kick.
39:36 The assistant referee signals for offside against Sam Williams. Willy Gueret takes the indirect free kick.
39:00 Unfair challenge on Nigel Quashie by Sam Williams results in a free kick. Free kick taken by Nigel Quashie.
38:11 The assistant referee flags for offside against Sam Williams. Indirect free kick taken by Willy Gueret.
37:27 The ball is crossed by Peter Leven, Steven Caulker manages to make a clearance.
35:47 Short corner worked by Jason Puncheon, clearance made by Shaun MacDonald. Outswinging corner taken from the right by-line by Nigel Quashie.
35:07 The offside flag is raised against Steven Caulker. Indirect free kick taken by Willy Gueret.
33:14 Free kick awarded for a foul by Peter Leven on Gavin Tomlin. Craig Alcock takes the direct free kick.
32:16 The assistant referee signals for offside against Sam Williams. Willy Gueret restarts play with the free kick.
31:00 The ball is swung over by Dean Lewington, Terrell Forbes manages to make a clearance. Free kick awarded for an unfair challenge on Sam Williams by Luke Howell. Direct free kick taken by Ryan Mason.
28:44 Free kick awarded for an unfair challenge on Aaron Wilbraham by Craig Alcock. Jason Puncheon sends in a cross, Darren Powell produces a header from inside the area that goes over the bar.
28:18 Sam Williams is penalised for handball and concedes a free kick. Willy Gueret restarts play with the free kick.
27:49 Unfair challenge on Ryan Mason by Luke Chadwick results in a free kick. Direct free kick taken by Craig Alcock.
26:24 Nigel Quashie has an effort at goal from outside the penalty box missing to the wide left of the goal.
25:12 Foul by Craig Alcock on Peter Leven, free kick awarded. Peter Leven takes the direct free kick.
23:55 Centre by Sam Baldock, clearance by Shaun MacDonald.
21:26 Gavin Tomlin produces a cross, Shot by Shaun MacDonald. Sam Baldock gets a block in. Corner taken by Shaun MacDonald played to the near post, Peter Leven makes a clearance.
21:26 Booking David McCracken is given a yellow card.
20:56 David McCracken gives away a free kick for an unfair challenge on Dean Bowditch.
19:23 Unfair challenge on Peter Leven by Gavin Tomlin results in a free kick. Peter Leven takes the direct free kick.
18:04 Centre by Craig Alcock, Peter Leven makes a clearance.
16:39 Gavin Tomlin provided the assist for the goal.
16:39 GOAL - Shaun MacDonald:MK Dons 1 - 2 Yeovil Shaun MacDonald fires in a goal from inside the penalty box to the bottom right corner of the goal. Milton Keynes Dons 1-2 Yeovil.
15:36 Corner taken by Jason Puncheon played to the near post, Shaun MacDonald makes a clearance.
14:41 Free kick awarded for an unfair challenge on Sam Williams by David McCracken. The free kick is swung in right-footed by Ryan Mason, clearance by Nigel Quashie.
13:12 Free kick awarded for an unfair challenge on Gavin Tomlin by Dean Lewington. Strike on goal comes in from Dean Bowditch from the free kick.
12:45 The ball is sent over by Craig Alcock, clearance made by Luke Howell.
12:19 Free kick awarded for a foul by Nigel Quashie on Dean Bowditch. Steven Caulker takes the free kick.
11:54 Sam Baldock takes a shot. Blocked by Steven Caulker.
8:02 Free kick awarded for an unfair challenge on Jason Puncheon by Nathan Smith. Luke Howell restarts play with the free kick.
7:04 Aaron Wilbraham is ruled offside. Free kick taken by Alex McCarthy.
6:14 Foul by Gavin Tomlin on David McCracken, free kick awarded. Nigel Quashie takes the free kick.
5:37 Dean Lewington gives away a free kick for an unfair challenge on Ryan Mason. Direct free kick taken by Craig Alcock.
4:26 The official flags Aaron Wilbraham offside. Free kick taken by Craig Alcock.
3:34 Aaron Wilbraham provided the assist for the goal.
3:34 GOAL - Sam Baldock:MK Dons 1 - 1 Yeovil Goal scored by Sam Baldock from just inside the penalty area to the bottom left corner of the goal. Milton Keynes Dons 1-1 Yeovil.
3:12 The referee blows for offside. Willy Gueret takes the free kick.
0:27 Assist on the goal came from Ryan Mason.
0:27 GOAL - Dean Bowditch:MK Dons 0 - 1 Yeovil Dean Bowditch finds the back of the net with a goal from the edge of the area low into the middle of the goal. Milton Keynes Dons 0-1 Yeovil.
0:00 The game gets underway.
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