Colin Larkin gave Town a first half lead and it looked as if the game was in the bag when Luke Gutteridge doubled the lead with 10 mins remaining.
Sunderland though fought back and scored on 85 mins through Anthony Stokes and the same player completed the comeback with the equaliser in stoppage time.
It was hard on Northampton in a game they deserved to win.
The match went to penalties with Leon Constantine seeing his kick saved by Marton Fulop.
An excellent effort but very unlucky.