Following the weekend storms, the Seagulls headed inland and recorded their first away win in seven games to boost their own prospects of making the play-offs.
Brighton battled back from going behind to a goal from Anthony Gerrard.
Nicky Forster equalised before the break with Glenn Murray grabbing a 78th minute winner.
Walsall had only themselves to blame. They carelessly wasted another golden opportunity to enhance their prospects when they struggled to overcome a Brighton side which had previously collected only one point from their previous six away games.
Walsall's lack of a goalscoring striker cost them dearly on the night when they were thwarted by Brighton goalkeeper Michael Kuipers, who distinguished himself with a fine save from a Lee Holmes early free-kick and then kept out attempts from Tommy Mooney, Kevin Betsy and Stefan Moore.
Kuipers, however, had little chance with a perfectly placed header from Gerrard in the 29th minute when the defender converted an accurate free-kick from Holmes.
Brighton, who should have gone ahead before Walsall's goal when Forster aimlessly shot wide, shocked the promotion chasing Saddlers with their 34th minute equaliser when Forster turned Ian Roper and produced a hopeful shot which surprisingly deceived the embarrassed Clayton Ince.
The Saddlers strived to break down Brighton's defence, but it was Murray who had the best chance for the Seagulls but his header in the swirling rain dipped over the bar.
But Murray was on the mark to bustle home Ian Westlake's left-wing cross to give the Seagulls their morale-boosting win.