The visitors had full-backs Rhys Weston and Netan Sansara sent off in the first half.
Jimmy Mullen's battling side made light of their numerical disadvantage to win with a goal just before the break from Dwayne Mattis.
Weston received his marching orders from referee Mike Thorpe only 15 minutes into the contest for a tackle on Brighton winger Dean Cox.
It looked a harsh decision against the former Cardiff defender, with Cox not requiring any treatment.
Sansara was dismissed in similar circumstances in the 33rd minute for a tackle on Brighton's other winger, Gary Hart.
Walsall still somehow managed to go in at half-time a goal up, thanks to a flick header from Mattis in the 44th minute from a free-kick by substitute Chris Palmer.
Brighton were camped inside Walsall territory after the break, but the Saddlers defended magnificently.
The home side came close to an equaliser in the 53rd minute when Glenn Murray's header from an inviting cross by Hart hit the top of the crossbar.
Former Coventry and Crewe keeper Clayton Ince was in fine form for Walsall.
The giant Trinidad & Tobago international's handling was exemplary as Brighton launched balls and bodies into the box.
Ince was so well protected by the back four that he did not have too many saves to make, although he did well to hold on to Murray's angled header from a corner by substitute Tommy Fraser 15 minutes from time.
Amazingly, it was Walsall's first clean sheet in 20 matches, while Brighton had still failed to win at home in the league this season.