Blackburn continued their impressive season as goals from Benni McCarthy and Morten Gamst Pedersen saw them reach the Carling Cup quarter-final.
McCarthy turned in Aaron Mokoena's cross after 11 minutes to give Mark Hughes' side the lead.
Blackburn then lost Mokoena with a suspected broken leg, while sub David Nugent missed an open goal for Pompey.
Pedersen added a close-range finish after 77 minutes, before Kanu pulled one back with a late header.
606: DEBATE
Blackburn grabbed the early ascendancy, with Christopher Samba heading David Bentley's corner over the top when unmarked.
But they did not have to wait long to break the deadlock when McCarthy was left unmarked to slide home Mokoena's cross from eight yards.
Blackburn suffered a serious blow after 26 minutes when Mokoena, who had just come back on after treatment, suddenly collapsed grabbing his leg and a stretcher was summoned.
Boss Mark Hughes had to make another change eight minutes before the interval when Bentley, who had been doubtful before kick-off, was replaced by Matt Derbyshire.
Portsmouth counterpart Harry Redknapp made a double change at the interval to try and inject life into his side, sending on Matt Taylor and Nugent for Noe Pamarot and Papa Bouba Diop.
But Nugent - who has had a miserable time since his £6m move from Preston - was guilty of a dreadful miss, heading wide from only a couple of yards with the goal at his mercy.
Blackburn hit back as they went for the crucial second goal, and Samba struck a powerful drive that was turned over the top by David James.
And the visitors did seal the victory with 13 minutes left when Pedersen stole in to score from six yards.
Kanu headed home in the dying seconds, but Blackburn hung on for the victory.
Portsmouth manager Harry Redknapp:
"We let in two poor goals and missed some chances as well. It's a shame because I would have loved a cup run.
"We lost to a good side. Blackburn are on a good run like ourselves."
Blackburn manager Mark Hughes:
"I took a lot of pleasure watching him. His retention of the ball and his work in tight areas was a joy to watch.
"He was always in there looking for scoring chances. He's back where he should be at."
Portsmouth: James, Johnson, Campbell, Distin, Pamarot (Nugent 46), Utaka, Diop (Taylor 46), Pedro Mendes, Davis, Kranjcar, Mwaruwari (Kanu 75).
Subs Not Used: Ashdown, Lauren.
Booked: Diop, Davis.
Goals: Kanu 90.
Blackburn: Friedel, Mokoena (Emerton 28), Samba, Nelsen, Berner, Bentley (Derbyshire 37), Khizanishvili, Dunn, Pedersen, McCarthy (Treacy 90), Santa Cruz.
Subs Not Used: Brown, Ooijer.
Booked: Berner, Dunn.
Goals: McCarthy 11, Pedersen 77.
Att: 11,788
Ref: Alan Wiley (Staffordshire).
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