Northeastern (19-10, 11-5 Colonial) led by 14 early in the second half after Quincy Ford hit Walker cutting through the lane for a thunderous dunk, and Walker added the free throw for a three-point play.
But Drexel reeled off 10 straight, including eight points from Tavon Allen, to make it 61-60 with 1:06 left.
Northeastern's Scott Eatherton made 1 of 2 after a non-shooting foul, and after a couple of Drexel misses, Mohamed Bah grabbed an offensive rebound and made a contested five-footer to tie it with 0.7 seconds left. He missed the and-one and Sammy Mojica missed the follow-up to force overtime.
Ford drilled a 3-pointer to make it 66-62 with 3:27 to go in overtime, then Walker made a three-point play, followed by a trey from Ford with 2:02 left to make it an eight-point game.
Damion Lee led Drexel (10-17, 8-8) with 30 points.