Charlie Austin's 14th goal of the season revived Swindon's promotion bid and ended Brighton's five-match unbeaten run.
The visitors lost goalkeeper David Lucas to a leg injury early on and Andrew Crofts almost took advantage with a low shot just wide of the post.
Glenn Murray saw a header cleared off the line and had a strong penalty shout rejected as Brighton piled on pressure.
But when Brighton failed to clear Mark Marshall's cross Austin found the net.
Brighton manager Gus Poyet told BBC Sussex:
"Unfortunately we didn't hit the target enough today. We had great opportunities to hit the target and we missed it completely. When you have your moments in the game, you have to score.
"They are in the promotion places because they've been organised, they've been good and they've been scoring goals when they needed to."
90:00+3:35 The referee blows his whistle to end the game.
90:00+1:44 Free kick awarded for an unfair challenge on Mark Marshall by Tommy Elphick. Alan Sheehan takes the free kick.
90:00+1:01 Kazenga LuaLua produces a left-footed shot from the edge of the box and misses to the right of the target.
89:46 Free kick awarded for a foul by Gary Dicker on Mark Marshall. Alan Sheehan takes the indirect free kick.
89:08 Charlie Austin challenges Tommy Elphick unfairly and gives away a free kick. Indirect free kick taken by Peter Brezovan.
88:04 Unfair challenge on Mark Marshall by Elliott Bennett results in a free kick. Indirect free kick taken by Alan Sheehan.
82:37 Free kick awarded for a foul by Tommy Elphick on Charlie Austin. Free kick taken by Jon-Paul McGovern.
80:49 Inswinging corner taken right-footed by Elliott Bennett, clearance by Gordon Greer.
79:12 Gary Dicker fouled by Simon Ferry, the ref awards a free kick. Elliott Bennett restarts play with the free kick.
78:50 Kazenga LuaLua fouled by Craig Easton, the ref awards a free kick. The free kick is swung in right-footed by Elliott Bennett, clearance made by Jonathan Douglas.
77:35 Tommy Elphick gives away a free kick for an unfair challenge on Jonathan Douglas. Shot comes in from Alan Sheehan from the free kick.
74:38 Substitution Nicky Forster is brought on as a substitute for Marcos Painter.
74:08 Free kick awarded for a foul by Adam El-Abd on Jon-Paul McGovern. Free kick taken by Alan Sheehan.
72:41 Foul by Charlie Austin on Tommy Elphick, free kick awarded. Indirect free kick taken by Peter Brezovan.
70:05 Substitution Alan Navarro leaves the field to be replaced by Chris Holroyd.
68:23 Jon-Paul McGovern provided the assist for the goal.
68:23 GOAL - Charlie Austin:Brighton 0 - 1 Swindon Charlie Austin gets on the score sheet with a goal from inside the penalty area to the bottom right corner of the goal. Brighton 0-1 Swindon.
66:32 Short corner taken by Elliott Bennett from the left by-line, Charlie Austin makes a clearance.
65:54 Corner from right by-line taken by Elliott Bennett.
65:16 Elliott Bennett takes a shot. Clearance made by Alan Sheehan.
64:33 Short corner worked by Alan Sheehan.
63:59 Corner taken by Alan Sheehan from the left by-line to the near post, Glenn Murray makes a clearance.
61:17 Foul by Inigo Calderon on Mark Marshall, free kick awarded. Free kick taken by Alan Sheehan.
57:58 Charlie Austin produces a right-footed shot from just outside the box that misses to the right of the net.
51:40 Inswinging corner taken by Alan Sheehan, save by Peter Brezovan.
48:24 Elliott Bennett concedes a free kick for a foul on Alan Sheehan. Free kick taken by Phil Smith.
47:40 Elliott Bennett produces a right-footed shot from just outside the area that goes wide left of the goal.
45:04 Substitution Craig Easton on for Daniel Ward.
45:01 The referee gets the second half underway.
Half Time
45:00+2:55 The referee blows for half time.
45:00+1:41 Simon Ferry concedes a free kick for a foul on Andrew Crofts. Alan Navarro takes the free kick.
45:00+0:48 Outswinging corner taken left-footed by Alan Sheehan from the left by-line, clearance made by Inigo Calderon.
45:00+0:27 Mark Marshall takes a shot. Save by Peter Brezovan.
40:59 Corner taken by Elliott Bennett from the right by-line, Alan Sheehan manages to make a clearance.
39:50 Gary Dicker takes a shot from just outside the penalty area clears the crossbar.
39:09 Corner from the left by-line taken by Elliott Bennett, clearance made by Alan Sheehan.
37:18 Glenn Murray fouled by Alan Sheehan, the ref awards a free kick. Free kick crossed right-footed by Elliott Bennett from right channel.
35:11 Elliott Bennett takes a inswinging corner to the near post, clearance made by Gordon Greer.
32:55 Foul by Charlie Austin on Tommy Elphick, free kick awarded. Tommy Elphick takes the free kick.
32:09 Substitution Vincent Pericard leaves the field to be replaced by Mark Marshall.
31:46 Free kick awarded for an unfair challenge on Gary Dicker by Jon-Paul McGovern. Free kick taken by Peter Brezovan.
31:10 Inigo Calderon gives away a free kick for an unfair challenge on Jonathan Douglas. Alan Sheehan restarts play with the free kick.
29:45 Elliott Bennett has an effort at goal from just outside the area which goes wide of the left-hand post.
28:41 Handball by Adam El-Abd. Free kick taken by Jon-Paul McGovern.
26:08 Glenn Murray takes a shot. Clearance made by Gordon Greer.
23:27 Daniel Ward challenges Glenn Murray unfairly and gives away a free kick. The ball is sent over by Elliott Bennett, Effort on goal by Glenn Murray from just outside the area goes harmlessly over the target.
22:57 Andrew Crofts challenges Jonathan Douglas unfairly and gives away a free kick. Scott Cuthbert takes the indirect free kick.
21:44 Andrew Crofts has an effort at goal from just outside the box which goes wide of the left-hand post.
20:50 The official flags Vincent Pericard offside. Indirect free kick taken by Peter Brezovan.
17:27 Daniel Ward takes a shot. Save made by Peter Brezovan.
16:57 Alan Sheehan takes a short corner.
14:57 Unfair challenge on Vincent Pericard by Alan Navarro results in a free kick. Jon-Paul McGovern takes the free kick.
13:53 Shot from deep inside the area by Daniel Ward clears the bar.
11:38 Substitution Phil Smith replaces David Lucas.
9:02 Charlie Austin fouled by Adam El-Abd, the ref awards a free kick. Alan Sheehan fires a strike on goal direct from the free kick, save by David Lucas.
7:23 The assistant referee flags for offside against Glenn Murray. David Lucas restarts play with the free kick.
3:52 Unfair challenge on Elliott Bennett by Alan Sheehan results in a free kick. Free kick taken by Inigo Calderon.
3:37 The assistant referee signals for offside against Glenn Murray. Free kick taken by Alan Sheehan.
2:32 Elliott Bennett takes a outswinging corner to the near post, Stephen Darby makes a clearance.
0:36 Corner taken by Elliott Bennett from the right by-line to the near post, clearance made by Alan Sheehan.
0:18 Kazenga LuaLua takes a shot. David Lucas gets a block in.
0:00 The game begins.
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Carlisle 1-3 Millwall
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