In a frenetic opening spell, Paul Merson chipped a delicate through ball for wing-back Matthew Taylor to latch on to and slot a low shot in to the corner of the net past Brighton keeper Andy Petterson.
But Brighton shocked the home side when Danny Cullip exchanged passes with Graham Barrett to drive past Shaka Hislop in the Pompey goal from 12 yards.
The Seagulls had the temerity to take the lead when Paul Brooker raced on to Richard Hughes' slack back-pass to shoot home from ten yards.
Portsmouth were stunned but drew level when Brighton debutant Guy Butters was adjudged to have man-handled Deon Burton in the penalty area. Merson made no mistake with the resultant penalty.
Portsmouth took control of the game and when Nigel Quashie's precision through ball found Taylor on the left, the wing-back's cross was tapped in by Svetoslav Todorov from close range on the stroke of half time.
Portsmouth carried on in the second half where they had left off in the first and after 52 minutes Jason Crowe raced clear to cut in and fire a spectacular shot in to the top left-hand corner of Petterson's net.
It threatened to turn into a rout when Todorov cut in and drove a shot at Petterson, but the former Pompey man continued to keep the Pompey forwards at bay.
Brighton's miserable afternoon in their first league clash at Fratton park for ten years was complete when on-loan Arsenal striker Barrett was sent off 14 minutes from time