The Cobblers started the brightest with Lawson D’Ath testing Matt Ingram and top scorer Marc Richards heading over. But Wycombe, who had to win to have any chance of securing automatic promotion, went closest when Paul Hayes hit the bar.
Northampton enjoyed plenty of possession but it was Wycombe who broke the deadlock in the 36th minute when the hosts failed to clear and Aaron Holloway volleyed home from 15 yards.
And the visitors took just three minutes to double their advantage when Hayes released Nico Yennaris who cut into the box and beat Shawn Jalal from a tight angle.
Rocked by the two-goal blast, Cobblers recovered and Richards went close just before the break when his header was kept out by Ingram.
And shortly after the restart D’Ath was denied by the Wycombe keeper while Joel Byrom’s goal-bound shot was kept out by Aaron Pierre as Northampton looked to get back into the contest.
Northampton reduce the arrears in the 67th minute when Ivan Toney’s low cross was sliced into his own net by Sam Wood. Alfie Mawson almost restored Wycombe’s two-goal advantage when his header was saved by Jalal.
But the visitors had to play out the closing stages without the injured Ingram with Alex Lynch taking over between the posts. Cobblers sensed a late point and D’Ath shot wide while Toney saw his effort blocked.
The equaliser finally arrived in the 85th minute when Ryan Cresswell’s looping header beat Lynch after Wycombe failed to clear. But Mawson scored the last-gasp winner when he struck home after Cobblers failed to deal with Steven Craig’s free-kick.