The Nigerian striker came on as a late substitute and provided Pompey with the cutting edge they had lacked for most of the Championship match, firing past Luke Steele with 10 minutes remaining to make it 1-0 at Fratton Park.
Barnsley had the first chance of the game after only two minutes, Danny Haynes latching onto a long ball but blasting over the bar.
Liam Lawrence then lofted a long ball for David Nugent, who found the space to force an impressive save from Steele.
In the ninth minute, Hayden Mullins made a mazy run into Barnsley's half before crossing for Dave Kitson, who took the cross in his stride but fired just wide of goal.
Debutant David Cotterill was instrumental in multiple forays into Tykes territory, consistently displaying a range of deft touches on the left wing.
Mark Robins' side began to look more dangerous after 20 minutes, dominating the midfield and keeping Kitson and Nugent under wraps.
Kitson's frustration soon showed as he scuffed a cross horribly wide and into the fans. In the 25 minute he had arguably his best chance to fire Pompey ahead, climbing to meet Greg Halford's free-kick but nodding just over.
Ten minutes before the break, Herman Hreidarsson produced a good block from another Haynes shot as the Tykes continued to carve open the home defence with probing passes.
Portsmouth's afternoon was soured even further as Lawrence was substituted before half-time, Aaron Mokoena his replacement.
In an attempt to reverse the tide, Pompey boss Cotterill switched his namesake winger onto the right wing. The Welshman responded by cutting inside and firing low at Steele, who did well to smother the shot.
The hosts were nearly given a boost one minute before the half-time whistle when substitute Mokoena wasted a good chance to score. Kitson fed the ball through to the South African who managed to scoop the ball over the bar.
Neither side could find an attacking rhythm after the restart, Kitson leaving it until the hour mark to test the goalkeeper again. The diminutive forward tricked his way behind the Barnsley backline but Steele was on hand to save smartly.
The home fans cheered the introduction of veteran striker Nwankwo Kanu in the 71st minute and his presence immediately sparked Pompey into life. He was unlucky not to put Mullins through on goal with one of his first touches of the ball.
After 83 minutes, the former Arsenal man proved his worth to Cotterill with the winning goal. Halford floated a ball into the box for Kanu to rise above Steele and head into the bottom corner.