Kanu scored an injury-time winner to earn Portsmouth a deserved win over Wigan in the FA Cup third round.
The half-time substitute headed home Glen Johnson's cross to condemn Wigan to their sixth straight defeat.
Wigan seemed to have earned a replay when Lee McCulloch equalised with an 83rd-minute strike after Andy Cole had put the home side ahead.
Cole scored after controlling a cross from Sean Davis and smashing the ball past Mike Pollitt with his left foot.
The handful of hardy Wigan fans who made the long trip south to sit in the rain and watch their team might feel that Kanu's late goal was cruel - but on the balance of play Pompey deserved their win.
Pollitt started in place of Chris Kirkland in the Wigan goal - and he was by far the busier keeper.
Cole had a shot blocked by Fitz Hall and then forced Pollitt into a tidy save, the Latics keeping diving low to his left, while Niko Kranjcar headed narrowly wide as Pompey started brightly.
Croatian midfielder Kranjcar drew another save from Pollitt after 20 minutes with a low free-kick and Kevin Kilbane later made a good defensive header with several Pompey players lurking.
Pompey's passing was, in the main, crisp and accurate, while their running on the ball was full of intent.
Wigan went into this tie in poor form - and without the influential duo of striker Henri Camara and former Pompey favourite Arjen de Zeeuw.
And the visiting team struggled to pressurise the reliable Pompey central defensive pairing of Linvoy Primus and Sol Campbell for most of the opening half.
Emile Heskey managed to head weakly over James' crossbar, while an atrocious cross-cum-shot from the normally reliable Leighton Baines was symptomatic of Wigan's struggle.
But Paul Jewell's team rallied before the break and almost scored when the ball broke loose in the Pompey area with Heskey closing in, but Campbell made a superb tackle.
Wigan played with more purpose after the break and the tie became a more even contest.
The visiting side forced a series of corners, one the consequence of a Denny Landzaat shot that was deflected wide.
But it was Pompey who struck the crucial opening goal, Cole wrong-footing Emmerson Boyce before scoring.
Baines came close to an equaliser with a long-range strike that James athletically saved but Pompey also created further openings, with Boyce clearing one strike off the line.
McCulloch then thought he had earned his side a draw, converting Gary Teale's cross, before Kanu's late strike stole the tie.
"I wasn't sitting on the edge of my seat at 1-0 up. I thought we would win 1-0 - but after McCulloch's great finish, it looked like a replay.
"But then Kanu came up with another goal. We are delighted."
"We came back well and could have nicked it. We are just unable to see games out at the moment, though.
"A replay would have presented difficulties, and I wanted us to go for the win. But I'd take a replay now - I just don't like losing matches."
Portsmouth: James, Johnson, Primus, Campbell, Taylor, O'Neil, Pedro Mendes, Davis, Kranjcar (Thompson 79), Cole, Mwaruwari (Kanu 46).
Subs Not Used: Ashdown, Griffin, O'Brien.
Goals: Cole 64, Kanu 90.
Wigan: Pollitt, Hall, Granqvist (Jackson 80), Boyce, Baines, Cotterill, Johansson, Landzaat (Haestad 66), Kilbane (Teale 70), Heskey, McCulloch.
Subs Not Used: Filan, Wright.
Booked: Hall.
Goals: McCulloch 83.
Att: 14,336
Ref: P Dowd (Staffordshire).