The game started with both teams struggling to create clear chances, with the biggest opportunity coming when Marshall Munetsi collected a loose ball and fed Hwang Hee-chan, but the South Korean player chose not to shoot and couldn't find a teammate.
Wolves' head coach Vítor Pereira received a red card for protesting the non-award of a free-kick to his team, but his players continued to play.
Wolves took the lead when Jhon Arias delivered a cross that was headed by Jørgen Strand Larsen, and Danny Welbeck failed to clear it, allowing Marshall Munetsi to score with a volley that was initially blocked by Bart Verbruggen but went in off his back.
Verbruggen made another crucial save by blocking Ladislav Krejčí's header, while at the other end, Jackson Tchatchoua's underhit pass to Sam Johnstone was almost capitalized on by Brajan Gruda.
Fabian Hürzeler substituted Georginio Rutter for Carlos Baleba at halftime, but it was Wolves who had the first big chance of the second half when Arias wasted a shot from Hugo Bueno's cutback.
Johnstone made a phenomenal save to block Rutter's effort from Yankuba Minteh's cross, but Wolves continued to face pressure from Brighton.
To shore up their defense, Emmanuel Agbadou replaced Hwang Hee-chan, but Wolves' approach seemed to invite more pressure, even if Brighton couldn't capitalize on their possession.
Against the run of play, Strand Larsen struck a post, and that moment proved pivotal as Wolves switched off from a short corner, allowing Jan Paul van Hecke to head in a goal from substitute Maxim De Cuyper's cross.
The result means that Brighton is now on a four-game unbeaten run in all competitions, while Wolves are struggling with another late goal, having been pegged back by Tottenham last weekend.
Wolves' top-flight head-to-head record against Brighton has now stretched to eight matches without a victory.