Latics looked like earning a hard earned point against an in-form Portsmouth team, but two late goals by Benjani and Glen Johnson sent Latics to defeat.
Benjani scored his seventh goal of the season with just nine minutes remaining to send Latics to defeat.
Sulley Muntari's left footed cross was perfect in finding his team mate, who easily converted from close range.
Glen Johnson then doubled the lead just minutes later when he latched onto a Benjani pass and planted a low shot into the corner of the net beyond the reach of Chris Kirkland.
After holding firm against a decent Pompey team, it was a bitter pill to swallow which leaves Latics without a win in two months.
But although the south coast club left the JJB Stadium with their fourth consecutive win, they were far from their best and it looked odds on that Latics would gain a goalless draw and a vital point.
Antonie Sibierski was recalled to the starting line-up after recovering from injury, and partnered Marcus Bent up front. Denny Landzaat also returned, and was made skipper in the absence of the injured Mario Melchiot.
Latics almost made an immediate impact from the kick-off and did have a clear cut chance as early as the second minute when Michael Brown's free-kick found Antonie Sibierski at the far post. The Frenchman flicked the ball back across the box to Paul Scharner whose header appeared to hit the woodwork. It was a promising start, but unfortunately that was the best chance of the first period.
In the 37th minute, Marcus Bent had a clear view of the target when he chased a ball down the right flank before racing into the penalty box, but his shot hit side netting.
As Latics suddenly went down two goals, substitute Julius Aghahowa had a chance in the last five minutes to half the deficit but his shot hit the side netting at the near post.
Until Pompey's late goal-scoring spree, Latics looked solid enough in defence to contain John Utaka and Benjani, and Titus Bramble prevented them from breaking the deadlock in the 71st minute he used his strength to great effect to stop the latter progressing into the penalty area.
The visitors passed the ball around well but did not trouble goalkeeper Chris Kirkland. The Latics shot stopper easily saved a long range Nico Krancjar effort in the 23rd minute, and then defender Glen Johnson saw his near post shot go wide moments later.
As the second half wore on, the visitors became more confident as they sent more forward to break down the Latics defence, and they passed the ball around confidently. Latics did manage to get forward on the counter-attack but struggled to test David James in the Portsmouth goal.
Just after the hour mark, Muntari went close as he drove a free-kick towards Kirkland from twenty-five yards, and it hit the woodwork. Later on Pompey substitute Pedro Mendes also had a chance as he drove a shot wide from twenty yards as Latics cleared a corner.
So Latics were unable to stop a high flying Pompey, but more points will be up for grabs next weekend as Latics travel to Birmingham.
LATICS: Kirkland; Boyce, Bramble, Granqvist, Kilbane; Landzaat (c), Brown, Scharner, Koumas; Bent, Sibierski (Aghahowa 52)
SUBS: Pollitt, Hall, Olembe, Skoko.
BOOKED: Aghaowa, Bramble
PORTSMOUTH: James; Johnson, Distin, Campbell (c), Hreidarsson; Diop, Davis (Mendes 77), Muntari, Kranjcar; Utaka, Benjani.
BOOKED: Campbell, Davis, Muntari
SUBS: Ashdown, Pamarot, Taylor, Mendes, Nugent.
BOOKED: Aghahowa
REFEREE: Howard Webb
