The Seagulls flew in to a sixth-minute lead when skipper Inigo Calderon stooped low to head in a corner from Elliott Bennett.
But Walsall threatened a surprise when their skipper Andy Butler headed his second goal of the season after 11 minutes. Tommy Elphick sliced a clearance high in to the air and the Saddlers defender headed home.
It took Brighton only two minutes at the start of the second half to regain their lead, with top scorer Glenn Murray rising unchallenged to head in his 22nd goal of the season from Bennett's corner.
Any hope Walsall had of saving the game were ended when Emmanuel Ledesma, playing against his former club, was shown a red card for a two-footed challenge on Brighton defender Adam El-Abd.
Brighton were comfortably in control when home goalkeeper Jimmy Walker kept out a drive from Murray, but in stoppage time Bennett burst forward to hammer a right-foot drive which flew past Walker as the Seagulls made it 11 wins in their last 12 games.