Dean Morgan thought he had fired home a 98th-minute winner was harshly adjudged offside.
Gareth Ainsworth made three changes to his side with Leon Johnson, Matt Bloomfield and Jo Kuffour replacing Nick Arnold, Marvin McCoy and Steven Craig - the latter two missing out through injury.
The visitors started the better of the sides and forced Wanderers back into their own half early on. Their impressive early play was to be rewarded in the 10th minute when Matt Ingram failed to deal with Ricky Ravenhill’s deep centre and the ball crossed the line before Blues’ No.1 could recover.
Alan Connell was then inches away from doubling Town’s lead as an overlap on the left created room for the forward and his well-struck effort flew just past Ingram’s post.
Blues’ first real chance came in the 15th minute, and in fortuitous circumstances, as a clearance struck Kuffour five yards out from goal, but the ricochet was straight at Matt Duke in the Northampton goal.
Wanderers were starting to come into the contest and their improved play forced an equaliser in the 18th minute. Skipper Stuart Lewis did well to win a free-kick on the right and Bloomfield’s inch-perfect set-piece was powered home by the head of Aaron Pierre.
Scowen fired wide from 25 yards, before Pierre almost repeated his earlier feat, as he again met a Bloomfield free-kick, but this time the Brentford loanee couldn’t keep his header down.
Ainsworth was forced into his first change on the half hour when Cowan-Hall limped off to be replaced by Dean Morgan.
Ingram produced a smart stop low to his left to palm away Connell’s 35th-minute free-kick. Northampton striker John Marquis was booked from the resulting corner as his high foot caught Scowen in the face as the midfielder bravely headed clear.
Bloomfield’s set-pieces were causing the visitors all sorts out of problems and Blues’ next chance came from another of these as McClure headed a free-kick wide at the far post five minutes before the break.
Lewis had a penalty appeal turned down in first-half injury-time after reaching Rowe’s clipped ball over the top ahead of the defender before going over in the area, and that was to be the final attack of the opening period.
Half-time: Blues 1-1 Northampton
Town started the second half as they had the first and enjoyed the majority of the early play, but it was the Chairboys who had the first clear chance in the 50th minute.
Patient build-up saw McClure find Wood on the left and his cross was met by Morgan, who saw his header crash back off the crossbar with Matt Duke well beaten.
Blues made their second change in the 61st minute when Pierre, who had been struggling with a shoulder injury, was replaced by Anthony Stewart.
Connell half-volleyed wide for the Cobblers after Horwood’s clever cross, but it wasn’t one-way traffic as McClure beat his marker to meet Bloomfield’s 70th-minute corner, however, his header just cleared the angle of post and crossbar.
Marquis fired well off target after former Wanderers loanee Hackett had flicked a long ball into his path.
The game was disrupted following a serious-looking injury to Northampton centre-back Zander Diamond, and upon resumption Lewis tried his luck from distance and Duke claimed at the second attempt.
Hackett shot harmlessly off target after Marquis showed good strength in the Wanderers area, before Ravenhill’s strike took a deflection, but was simple for Ingram.
Referee Andy D’Urso added on 10 minutes for the injury to Diamond and another for Johnson.
McClure had a penalty shout turned down when he looked to have got the other side of his marker. Both sides pushed forward in search of a dramatic winner and Blues thought they had found it in the eighth minute of injury-time.
Kretzschmar’s curled a superb free-kick over the wall, only for it to rebound back off the bar. The ball fell to Johnson, who hooked back across and goal and Morgan fired home, but was flagged for offside.
Wanderers: Ingram, Rowe, Wood, Johnson, Pierre (Stewart 61), Cowan-Hall (Morgan 30), Lewis (c), Scowen, Bloomfield, McClure, Kuffour (Kretzschmar 90).
Subs: Horlock, Arnold, Stewart, Kretzschmar, Morgan, Morias, Jeffrey.
Attendance: 7,004 (2,125 away)