Kanu came up trumps yet again for Portsmouth with a last-gasp header that took his goal-tally for the season into double figures and knocked battling Wigan out of the FA Cup.
Kanu had started on the bench in an attempt to rest his tired legs after a crowded Christmas and New Year but proved his qualities once again with a trademark finish after Lee McCulloch's stunning 83rd-minute strike appeared to earn a replay for the visitors.
Earlier Andy Cole, starting only his fourth Pompey first-team game, looked to be the match-winner as he rolled back the years with an electric 64th-minute finish.
The 35-year-old former England marksman turned Emerson Boyce as he controlled a Glen Johnson cross and crashed a drive into the top-left hand corner for his fourth of the campaign.
He showed strike partner Benjani Mwaruwari how to do it. Benjani's goal beat Wigan at Fratton Park in September and the visiting fans were clearly not all that confident of revenge. Barely a few hundred took up places in the away end at Fratton Park.
But the big Zimbabwean was kinder to them this time, landing a shot among their sparse number in the 36th minute when skipper O'Neil presented him with the kind of opportunity he should have buried instead of skying over the bar.
Sadly it was typical profligacy by the striker who has brought such industry and determination to Harry Redknapp's team but this time he was not the only one to miss his chance.
Pompey peppered the Wigan goal right from the start but there were bad omens in the eighth minute after Andreas Johansson handled 35 yards from goal and Matt Taylor scuffed the free kick disappointingly wide - nothing like some of his recent long-range specials.
Swedish newcomer Andreas Granqvist showed early signs of struggling to judge the pace of the game when allowing a through ball in the 13th minute to run past him for Benjani. He rounded Pollitt and looked certain to hit the net with his shot until Granqvist got back to clear it away and make amends.
But Granqvist looked a shaky replacement for veteran Arjan de Zeeuw whose defensive brilliance has benefited both sides during his career.
Wigan also rested £2.5million keeper Chris Kirkland but Pollitt proved a good stand-in, holding drives from Cole and Sean Davis
Cole also had a shot blocked by Fitz Hall and when Johnson rebuilt the move with a clever cross, Niko Kranjcar's glancing header was just wide of the near post.
Cole looked sharp and Pollitt had to turn his studied drive around a post for a corner in the 17th minute after O'Neil supplied the pass and as the rain poured down Wigan had to absorb a wave of attacks.
But after Benjani's big miss nine minutes before the interval it was hardly a surprise to see him replaced by Kanu for the second half.
For a while Pompey's prospects of turning their superiority into a place in the fourth round looked no better but in the 64th minute Cole came up with something special.
Johnson's low cross from the right was allowed to travel right across the face of the penalty area where Cole, in an old-fashioned inside left position, took one touch to turn Boyce and blast an unstoppable shot in the top near-post corner of the net.
Under-worked Pompey goalkeeper David James had to make his best save of the match to deny Leighton Baines' fizzing drive soon afterwards but there seemed little danger to Pompey despite a trio of Wigan substitutions.
And Boyce had to clear O'Neil's shot off the line after Pollitt parried Davis' effort.
McCulloch, just back from suspension, had other ideas though. The Scot drilled in David Cotterill's cross and seemed to have saved the tie - especially after Cole and O'Neil got in each other's way as they tried to force home an even later decider.
But then came Kanu - courtesy of an other Johnson cross - with a typical finish and Wigan were left to sort out their latest setback.
Teams:
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).