Dean Hammond's early penalty and a second-half header by Alex Revell earned the south coast club their first win at Withdean since beating Nottingham Forest in February.
They made an ideal start as Northampton conceded a needless penalty with only 52 seconds on the clock.
Revell got a toe to a low cross from Jake Robinson and Chris Doig brought him down.
Skipper Hammond, who gave away a penalty in Brighton's opening day defeat at Crewe, rammed the resulting spot-kick into the roof of the net.
That should have filled the home side with confidence, but they lost their way and Northampton deservedly levelled midway through the first half.
Northern Ireland international striker Andy Kirk headed in a right-ring cross from Jason Crowe for his third goal in as many games.
The visitors threatened to take charge and Brighton's Dutch goalkeeper Michels Kuipers was forced into making smart saves from Andy Holt and Poul Hubertz before the break.
Brighton regrouped and were rewarded after manager Dean Wilkins changed tactics in the second half by moving Dean Cox from the right into the middle of midfield and Robinson switching wings to the left.
Revell clinched the points in the 66th minute when he rose highest to nod in a curling free-kick from Sam Rents.
Brighton could have gone on to win more convincingly as tempers flared and Northampton lost their heads.
Revell's shot was cleared off the line by Mark Hughes when Nicky Forster intercepted Doig's short back-pass, then Forster shot straight at keeper Mark Bunn on his home debut following his summer move from Hull.
Hammond was stretchered off in the closing stages with a gashed knee after running into the sturdily-built Doig.