Defender Tommy Elphick rescued a point for managerless Brighton.
Ryan Gilligan drove the Cobblers ahead from 20 yards on the stroke of half-time as the visitors looked to end a run of four successive defeats.
Elphick struck 12 minutes after the break by heading in an outswinging corner from substitute Seb Carole.
Both sides finished with 10 men as Brighton's Adam Virgo and Adebayo Akinfenwa of Northampton were sent off following a tangle on the halfway line.
Brighton: Kuipers, Whing, El-Abd, Elphick, McNulty, Birchall (Davies 52), Fraser (Carole 55), Jarrett, Cox, Forster, Virgo. Subs Not Used: Sullivan, Hinshelwood, McLeod.
Sent Off: Virgo (65).
Goals: Elphick 57.
Northampton: Zieler, Rodgers, Hughes, Doig, Crowe, Gilligan, Dyer, Osman, Holt, Constantine, Akinfenwa. Subs Not Used: Dunn, Coke, Larkin, Clarke, Dolman.
Sent Off: Akinfenwa (65).
Booked: Doig, Dyer.
Goals: Gilligan 45.
Att: 5,062
Ref: Trevor Kettle (Rutland).
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