Benjani's goal early in the second half settled a dull game in the home side's favour to keep Harry Redknapp's men flying high at the top of the Premiership.
Redknapp left all three of his transfer deadline day signings - Andy Cole, Rodolph Douala and Niko Kranjcar - out of his 16-man squad.
Pedro Mendes was back in the starting line-up only 17 days after falling victim to Ben Thatcher's brutal elbow attack, while Glen Johnson also returned after an ankle injury.
Wigan named £2million new signing David Cotterill on the bench, but Henri Camara was fit to start after recovering from a minor knock.
Portsmouth came into games knowing a win could take them top of the Premiership table for a couple of hours at least, but the first half failed to live up to its billing.
Home striker Benjani had the first sight of goal in the fifth minute when his 20-yard shot was well charged down by Fitz Hall.
Camara gave the Pompey defence a nervy moment midway through the first half when he got in behind only for the returning Mendes to get back and deflect his shot over the bar.
Camara won Wigan a cheap free-kick with six minutes of the half remaining when he was clipped by Linvoy Primus on the edge of the area, but Denny Landzaat fired the ball straight into a grateful Pompey wall.
Matt Taylor caught Wigan goalkeeper Chris Kirkland napping in first-half stoppage time with a teasing left-wing cross that was misjudged by the on-loan Liverpool star, but in keeping with the half there was no one on hand to take advantage as the ball broke free at the back post.
Emile Heskey came close to breaking the boredom a couple of minutes after the restart when he rose to head inches wide of David James' goal from Antonio Valencia's free-kick.
Wigan found themselves behind a matter of second later when record buy Benjani notched his second goal in as many matches to put the home side in front.
Benjani raced on to Sol Campbell's long ball over the top and shrugged off the challenge of both of Wigan's central defenders before clipping a sweet side-footed shot in off the inside of the left-hand post.
Pompey almost lost their status as the only team in the country yet to concede a goal on the hour-mark when Camara blazed over from the edge of the area after being teed up by Heskey.
James was forced into his first meaningful save of the afternoon four minutes later when he parried away Landzaat's right-foot shot from the edge of the box.
Pompey were forced into a change in the 66th minute when captain Dejan Stefanovic hobbled off to be replaced by Noe Pamarot.
Pamarot almost gifted Wigan an equaliser within minutes of coming on when he under-hit a back pass and James came scrambling out of his goal to save at the feet of Camara.
James was left exposed again in stoppage time when Campbell failed to cut out a high ball into the box but the former England number one just managed to beat Paul Scharner to the ball.