The striker, who Wigan tried to sign on loan before his move to Pompey last year, struck after 81 minutes scoring from inside the six-yard box after Chris Kirkland hesitated in dealing with the cross from Sulley Muntari.
And Portsmouth wrapped it up with a spectacular goal from Glen Johnson four minutes later as the Wigan defence fatally backed off.
It was total disaster for the Latics - their fourth defeat in a row - and the pressure really is on Chris Hutchings to get results after two months without a win.
The Latics had Denny Landzaat back and he also took over the captaincy from the injured Mario Melchiot. Antonio Valencia was also missing but Hutchings welcomed back striker Antoine Sibierski.
Wigan were inches away from a dream start as Pompey were saved by the woodwork, Michael Brown swung in the free-kick from the right, it was nodded back inside by Andreas Granqvist and Paul Scharner's header came back off the post.
Despite some neat play, Pompey were restricted to long-range shots. Papa Bouba Diop and Johnson both missed the target, but Niko Kranjcar forced Chris Kirkland to his knees to make the save.
Latics hit back when a Scharner flick-on sent Marcus Bent racing in on goal but he hammered the shot into the side netting. And the ex-Charlton striker was unlucky to find himself on the receiving end of a marginal offside decision when he again went clear.
There was more anxiety for Portsmouth when Muntari was adjudged to have fouled Sibierski just outside the box, but Jason Koumas hit the free-kick well over the bar.
Sean Davis felt he should have had a penalty when he went down in the Wigan area and there was a blow for Latics when Sibierski had to be replaced by Julius Aghahowa.
The Nigerian instantly had a couple of minutes to remember - collecting a booking within seconds and then needing treatment for a bang on the head.
Sol Campbell failed to make a chance count when he put a header wide and Muntari clipped the post with a terrific free-kick from long range.
But Portsmouth struck twice in four minutes to kill Wigan off with those strikes from Benjani and Johnson sending their army of supporters wild and Latics' fans heading for the exits.