For Reading it was a dreadful start, conceding a penalty and having a player sent off after just three minutes.
The Royals were caught out by a long ball forward to Benjani, who was clearly tripped inside the penalty area by Reading central defender Ibrahima Sonko as he bore down on goal.
It was the third penalty Sonko has conceded in Reading's last four games and referee Mike Dean showed him a red card, leaving the home side to face 87 minutes with only ten men.
Niko Kranjcar stepped up to take the kick, but his shot hit the upright and was eventually hacked away to safety by Nicky Shorey.
Reading showed that they intended to put up a fight against the odds and came close to equalising moments later. Kevin Doyle created an opening for Bobby Convey, but the American midfielder's left-foot effort was sliced wide of the post.
It was Convey's last act of the game because Reading boss Steve Coppell replaced him with central defender Andre Bikey in an effort to shore up his defence.
It didn't work, because just a couple of minutes later Portsmouth took the lead thanks to another dreadful Reading blunder. Goalkeeper Marcus Hahnermann made a complete hash of Sulley Muntari's free-kick and Papa Bouba Diop headed down to Sol Campbell, who poked the ball over the line.
There were Reading claims that Campbell had both handled the ball and was in an offside position, while Portsmouth pointed to a possible hand-ball by Reading midfielder Kalifa Cisse, but Mr Dean was happy to let the goal stand.
Try as they might Portsmouth were unable to stretch their lead before the break and Reading might even have grabbed an equaliser. Stephen Hunt and Doyle combined to set up a chance for Doyle. David James was quick to spot the danger and managed to get enough of his body behind the Irishman's shot to divert it for a corner.
Inevitably Portsmouth's 11 men eventually made another breakthrough and it came in the 66th minute.
A long all out of defence saw John Utaka outpace England international full-back Shorey, skip to the side of Hahnemann and steer the ball into the empty net.
Shorey, who had been suffering with a stomach problem for several days, was quickly replaced by substitute Ulises De la Cruz.
Portsmouth certainly deserved the points, but the fact is that Reading were up against it from the moment Sonko was dismissed at the start of the game.