Chris Iwelumo's early goal set them on the way and Dennis Lawrence sealed it by heading into his own net soon after half-time.
Albion manager Mark McGhee led his players in a tribute to 900 supporters who had made the 260-mile trip to North Wales. A small number of Wrexham supporters held up red-cards protesting against chairman Mark Guterman, but hundreds more streamed onto the pitch and surrounded their own heroes who had only a mid-table place to show for the season's efforts.
"It's been a great win today for our supporters," McGhee said.
"We look forward to starting at Swindon in the play-offs, just up the M4. It's going to be a tremendously difficult game for us but in our present form we should win.
"My European experience tells me that its very important and the right way round to get the second leg at home. We are not promoted yet. The hardest part is yet to come." Wrexham manager Denis Smith was disappointed to wrap up the league season with a defeat, but said he had to be content with a reasonable achievement against a background of injuries and cash problems.
He added: "Brighton were not interested in coming out after the second goal. They played deep and kept eleven men behind the ball." Iwelumo missed an early chance, shooting straight at Mike Ingham but he made amends when he headed home from a flick-on by Adam Virgo to score his first goal in six games.
Chris Llewellyn headed against Albion's crossbar before Lawrence sank his side, heading into his own net as he tried to clear Virgo's cross.