Vale's first win in 11 games boosted their slim hopes of survival as sad Pompey ended the game with nine men.
Defenders David Waterman and Adrian Whitbread both received their marching orders as Portsmouth's four-match winning run came to an end.
Vale, desperate for victory, went ahead with their first serious attack in the 15th minute.
David Healy and Michael Cummins swapped passes to set up Ville Viljanen and the Finnish striker hammered a shot in off the bar from close range.
The goal did wonders for Vale's spirit and Vinjanen squandered a great chance to add a second five minutes later.
Tommy Widdrington dinked a neat chip into the danger zone and Viljanen snatched his shot wide with the goal at his mercy.
Portsmouth weathered the storm to fight back and came within inches of a 34th minute equaliser.
Kevin Harper showed Allen Tankard a clean pair of heels to fire a cross-cum-shot which Kevin Pilkington tipped onto the crossbar.
But Vale were playing with real spirit and the contest took a massive turn their way two minutes before the break.
Viljanen's volley was handled by Waterman and referee Paul Rejer pointed to the spot and showed the Portsmouth defender the red card.
Widdrington sent Russell Hoult the wrong way to bury the penalty and give resurgent Vale a 2-0 interval lead.
Vale were untroubled in the early stages of the second half and Portsmouth made a double substation in the 62nd minute with Jason Crowe and Andy Awford entering the fray.
Awford's inswinging corner almost led to a goal within moments as Darren Moore flicked on and Steve Claridge just failed to convert at the far post.
And it really looked to be Vale's day when Shaun Derry contrived to sky the ball over an empty net from three yards from Awford's 65th minute free-kick.
Portsmouth's misery was complete seven minutes from time when Whitbread was sent off for a second yellow card.