Dowie looked to be heading for a vital three points as Hull led 2-1 with only two minutes remaining. But Jamie O'Hara levelled in the 88th minute before a defensive mistake by Richard Garcia let in veteran former Arsenal striker Kanu to score the winner.
Hull started brightly enough with Jan Vennegoor of Hesselink hitting a post before Dowie was out of his touchline seat celebrating in the 27th minute.
Caleb Folan's shot appeared to take more than one deflection on its way past David James in the Portsmouth goal.
Pompey, docked nine points earlier in the week and seemingly doomed to relegation, stormed back to level ten minutes later.
Hermann Hreidarsson headed a centre back across goal for former Watford striker Tommy Smith to score his first Pompey goal from close range.
Hull always looked the side most likely to get a second goal and Folan, who had previously scored once in 19 appearances, slotted in his second of the afternoon after 73 minutes from Garcia's pass.
Danny Webber went close for Portsmouth before O'Hara's superb free-kick appeared to have deprived Hull of a much-needed point.
But then Garcia's blunder let in Nadir Belhadj to set up Kanu and Hull were left with nothing.
Dowie had earlier made three changes in selecting his first Hull side but felt his team had suffered from losing inspirational captain Andy Dawson. Garcia replaced him.
Portsmouth manager Avram Grant had threatened to send out a weakened team in protest at the Premier League's decision to dock the nine points.
Grant did make five changes from the team beaten at Liverpool on Monday although one of those saw the return in goal of calf-muscle injury victim James in place of Jamie Ashdown.