Their fourth win in six games was well deserved and they should have scored a hatful as Brighton's play-off hopes suffered a severe blow.
Vale started the game brightly and they went ahead in the 12th minute. Danny Whitaker's cross reached Marc Richards at the far post and, although he scuffed his first effort, he still had time to score with a low drive.
Richards added his fourth goal in three games seven minutes later. The former Barnsley centre-forward burst through Brighton's ponderous defence to prod past keeper Michels Kuipers.
Brighton, strangely out of sorts, were back in the match in the 26th minute. Dean Cox latched on to a flick by Glenn Murray to convert his first goal since November with a left-foot shot low into the bottom corner.
Vale should have been out of sight by half-time. Richards and Krystian Pearce both missed the target with headers, while Kuipers also denied Whitaker and the rampant Richards with smart saves.
Cox should have equalised early in the second half for Brighton, but slotted wide when clean through.
If that was a let-off for Vale, Whitaker was left hanging his head in disbelief as the woodwork denied him three times in as many minutes as he first struck the outside of a post and then the crossbar twice.
Brighton centre-half Tommy Elphick also headed against his own crossbar and, after surviving so many escapes, Brighton threatened to snatch an unlikely point.
Vale keeper Joe Anyon had to save from Nicky Forster and substitute Joe Gatting before justice was done two minutes from time, Whitaker swivelling to score in spectacular fashion from 30 yards.
Murray headed in an injury-time consolation for shell-shocked Brighton from a Cox cross. He also nodded in a Kerry Mayo centre moments later, but it was disallowed for pushing by ref Paul Armstrong.
There were no complaints from the Brighton players and there could be no complaints either about their first home league defeat in ten matches.