Northampton, who named returning top scorer Marc Richards on the substitute's bench, had the better of the play in the first half and took the lead through Ryan Cresswell's header just after the half hour mark.
Chris Wilder's side restricted their hosts to only a handful of sights on goal and looked to have survived the late dismissal of Gregor Robertson for a second yellow card as well as a lengthy period of stoppage time to claim the victory.
Aaron Holloway, however, scored in the 98th minute of the game, sparking a flurry of yellow cards on both sides as the afternoon ended controversially.
Reaction: Wilder was in philosophical mood afterwards both about Robertson's red and the melee which followed Wycombe's goal.
"The incident at the end is part and parcel of the game. These are two passionate teams and two managers who want to go and get a result and I'm all for that.
"It was a difficult game for the referee - but he's human and he calls a match as he sees it."