Ryan Gilligan's first-half goal was enough for Northampton to see off a Stevenage side who were forced to play the last 38 minutes with 10 men.
Gilligan fired the visitors ahead when he latched on to Liam Davis's pass to rifle the ball past Chris Day.
Boro's hopes were hit when half-time substitute Darius Charles saw red for a professional foul on John Johnson.
Yemi Obudabe, Ben May and Josh Walker all went close for the hosts but the Cobblers held on for a deserved win.
Stevenage manager Graham Westley told BBC Three Counties Radio:
"There are a number of things that will be talking points from the game, the sending-off being a big one.
"I was also disappointed we had the goal disallowed. Their boy on the post said it crossed the line by a yard.
"But the start to the first half wasn't good enough. We conceded the goal which was unlike us, and in the end, because of all those circumstances we paid the price."
Northampton Town manager Ian Sampson told BBC Radio Northampton: "I'm really pleased. It's a tough place to come and Stevenage are a strong outfit.
"In the first half, we put some good passages of play together and scored a cracking goal.
"I've got to thank my goalkeeper for keeping us in it."
Live text and stats
Saturday, 11 December 2010
Npower League Two
Home Team
Score
Away Team
Time
Stevenage
0-1
Northampton
FT
(HT 0-1)
Gilligan 14
Stevenage
16 Day
02 Wilson (Dixon 77)
03 Laird
05 Ashton
14 Roberts (Charles 46 red card)
25 Henry
21 Mousinho
24 Bostwick yellow card
28 Walker
12 May (Odubade 46)
15 Holroyd
Substitutes
01 Bayes,
04 Charles,
18 Bridges,
22 O'Shea,
11 Odubade,
20 Beardsley,
26 Dixon
Northampton
01 Dunn
06 Beckwith
14 Johnson (Rodgers 55)
25 Tozer yellow card
04 Thornton
07 Gilligan
11 Holt
12 Wedderburn
23 Davis
16 McKay yellow card (McKenzie 79)
30 Jarvis (King 67)
Substitutes
13 Walker,
02 Rodgers,
03 Hall,
17 Jacobs,
15 Herbert,
18 McKenzie,
28 King
Ref: HorwoodAtt: 3,128
STEVENAGE
NORTHAMPTON
Possession
Stevenage44%
Northampton56%
Attempts on target
Stevenage3
Northampton3
Attempts off target
Stevenage7
Northampton4
Corners
Stevenage7
Northampton5
Fouls
Stevenage15
Northampton8
Final Result
90:00+5:55 Floated corner taken by Josh Walker, save by Chris Dunn.
Full Time
90:00+5:25 The final whistle goes and the game is over.
90:00+4:59 Corner taken by Josh Walker played to the near post.
90:00+4:01 Headed effort from deep inside the penalty area by Chris Holroyd misses to the left of the goal.
Correction - 90:00+2:21 Ryan Gilligan challenges Chris Holroyd unfairly and gives away a free kick. Shot on goal comes in from Josh Walker from the free kick,
90:00+2:21 Free kick awarded for a foul by Ryan Gilligan on Chris Holroyd. Josh Walker fires a strike on goal direct from the free kick,
90:00+0:48 Free kick awarded for a foul by Ronnie Henry on Craig King.
89:46 John Mousinho takes a shot. Blocked by Ben Tozer.
89:13 Ben Tozer concedes a free kick for a foul on Yemi Odubade. Indirect free kick taken by Josh Walker.
89:13 Booking Ben Tozer receives a caution.
87:01 Foul by Terry Dixon on Kevin Thornton, free kick awarded. Ben Tozer takes the free kick.
84:49 Josh Walker takes a shot. Save by Chris Dunn.
84:09 Liam Davis has an effort at goal from just inside the box that misses to the right of the target.
82:13 Corner taken by Josh Walker from the right by-line, Ben Tozer concedes a free kick for a foul on Ronnie Henry. Ronnie Henry restarts play with the free kick.
81:45 Josh Walker takes a outswinging corner to the near post, Liam Davis makes a clearance.
80:00 Corner taken by Josh Walker.
78:06 Free kick awarded for an unfair challenge on Billy Mckay by Michael Bostwick. Ryan Gilligan delivers the ball from the free kick right-footed from left wing, clearance by Jon Ashton.
78:06 Substitution Billy Mckay leaves the field to be replaced by Leon McKenzie.
77:43 Craig King produces a header from close range which goes wide of the left-hand upright.
76:15 Substitution Terry Dixon is brought on as a substitute for Lawrie Wilson.
74:54 Free kick awarded for a foul by Jon Ashton on Ryan Gilligan. Kevin Thornton crosses the ball from the free kick left-footed from left channel, Scott Laird manages to make a clearance.
73:15 Free kick awarded for a foul by Nathaniel Wedderburn on John Mousinho. Ronnie Henry restarts play with the free kick.
71:21 Corner taken right-footed by Ryan Gilligan from the left by-line to the near post, save by Chris Day.
70:09 Billy Mckay takes a shot. Chris Day makes a save.
69:35 Yemi Odubade gives away a free kick for an unfair challenge on Paul Rodgers. Ben Tozer takes the indirect free kick.
67:40 Ronnie Henry gives away a free kick for an unfair challenge on Liam Davis. Indirect free kick taken by Kevin Thornton.
66:58 Substitution Craig King joins the action as a substitute, replacing Ryan Jarvis.
63:52 Ryan Gilligan gives away a free kick for an unfair challenge on Scott Laird. Josh Walker crosses the ball in from the free kick, clearance made by Liam Davis.
59:47 Nathaniel Wedderburn fouled by Lawrie Wilson, the ref awards a free kick. Ryan Gilligan takes the indirect free kick.
58:53 Dean Beckwith is adjudged to have handled the ball. Indirect free kick taken by Ronnie Henry.
58:09 Short corner taken by Andrew Holt, Dean Beckwith has a headed effort from close range and clears the crossbar.
57:34 Corner from the right by-line taken by Kevin Thornton, clearance by Jon Ashton.
56:46 Free kick awarded for an unfair challenge on Liam Davis by Lawrie Wilson. Ryan Gilligan restarts play with the free kick.
56:00 Josh Walker challenges Ryan Gilligan unfairly and gives away a free kick. Ben Tozer takes the indirect free kick.
55:35 Yemi Odubade takes a shot. Chris Dunn makes a save.
55:01 The referee blows for offside.
51:24 Free kick awarded for a foul by Darius Charles on John Johnson. Indirect free kick taken by Ben Tozer.
51:24 Substitution John Johnson leaves the field to be replaced by Paul Rodgers.
51:24 Sent off Darius Charles is shown a red card for professional foul.
47:47 Ryan Jarvis gives away a free kick for an unfair challenge on Michael Bostwick. Free kick taken by Josh Walker.
46:53 Chris Holroyd is flagged offside by the assistant referee. Indirect free kick taken by Chris Dunn.
46:02 Josh Walker takes a inswinging corner.
45:01 The second half begins.
45:01 Substitution Yemi Odubade on for Ben May.
45:01 Substitution Darius Charles on for Mark Roberts.
Correction - 45:00+4:27 The referee calls an end to the first half.
Half Time
45:00+3:15 The players leave the pitch at half time.
45:00+1:54 Ben May challenges John Johnson unfairly and gives away a free kick. Ben Tozer takes the free kick.
44:30 Nathaniel Wedderburn is penalised for a handball. Strike comes in from Josh Walker from the free kick.
44:30 Booking Billy Mckay goes into the book for not retreating ten yards at a set play.
41:21 Free kick awarded for an unfair challenge on John Johnson by Scott Laird. The free kick is delivered right-footed by Ryan Gilligan from right wing, Ben May makes a clearance.
35:54 Corner taken by Josh Walker from the left by-line to the near post, Scott Laird takes a shot. Liam Davis gets a block in.
33:36 Ben May has a headed effort at goal from close in which goes wide left of the goal.
30:28 Unfair challenge on Dean Beckwith by Ben May results in a free kick. Ben Tozer takes the indirect free kick.
29:19 Shot on goal by Chris Holroyd from just inside the area clears the crossbar.
26:45 Close range header by Chris Holroyd goes over the crossbar.
25:13 Ben May fouled by John Johnson, the ref awards a free kick. Scott Laird restarts play with the free kick.
22:29 Dean Beckwith concedes a free kick for a foul on Ben May. Chris Day takes the free kick.
21:29 Free kick awarded for an unfair challenge on John Johnson by Michael Bostwick. Ben Tozer restarts play with the free kick.
21:29 Booking Michael Bostwick booked.
19:31 Ryan Jarvis takes a shot. Chris Day makes a save.
19:04 Inswinging corner taken from the right by-line by Kevin Thornton.
18:05 Kevin Thornton takes a inswinging corner from the right by-line played to the near post, Josh Walker manages to make a clearance.
13:17 The assist for the goal came from Liam Davis.
13:17 GOAL - Ryan Gilligan:Stevenage 0 - 1 Northampton Ryan Gilligan fires in a goal from close range to the bottom left corner of the goal. Stevenage 0-1 Northampton.
9:42 John Johnson is flagged offside by the assistant referee. Indirect free kick taken by Chris Day.
5:49 Ryan Jarvis takes a shot. Blocked by Ronnie Henry.
2:51 Kevin Thornton fouled by John Mousinho, the ref awards a free kick. Direct effort from the free kick comes in from John Johnson.
0:56 Lawrie Wilson is flagged offside by the assistant referee. Chris Dunn takes the indirect free kick.
0:00 The ref blows the whistle to begin the match.
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