Steve Cotterill's men dominated long periods of the game and had nineteen attempts on goal compared to Hull's five, two of which were on target and yet both found the back of the net along with Jimmy Bullard's penalty.
Pompey had many chances in the first half, amongst them being two Nugent shots, a Liam Lawrence free kick that hit the crossbar and then Kanu put a free header wide from Nugent's cross.
Jimmy Bullard also hit the upright with his free kick before giving his side an undeserved and controversial lead after Greg Halford, available as Portsmouth are appealing his red card, was judged to have tripped Cameron Stewart.
The Snood-wearing Hull midfielder looked to have gone down very easily in the box even if Halford did look like he barged into him slightly. Bullard made no mistake in firing the spot kick past Ashdown, sending him the wrong way with a powerful shot.
Behind once again, the men in blue wasted no time in trying to get back into the game as a succession of headers from crosses were missed as the whistle blew with Pompey fans wondering how their side were not ahead, let alone losing.
The second half followed much of the same pattern as Pompey dominated possession and found a lot of joy down Hull's right hand side with Utaka giving Nobby Solano a torrid time.
However, the Nigerian failed to hit the target with Hull 'keeper Brad Guzan gathering his first weak effort and the other of his shots fired wide.
But Pompey eventually equalised when Lawrence was brought down by Anthony Gerrard in the box and the Irishman powered his penalty past Guzan. From then on it looked like only one side were going to go on and win it but the hosts were about to be hit by two sucker-punches.
Substitute and debutant Matty Fryatt was given far too much time and space in the box following a quick Hull counter-attack and the former Leicester man slotted past Ashdown.
Then, just three minutes later, another substitute in Nick Barmby was allowed to get close enough to the Pompey goal to turn in the box and fire in a third to stun Fratton Park.
Pompey continued to show character by continuing to attack and pulled a goal back when Halford headed in a corner with just less than 15 minutes to go.
There were chances to earn a well deserved draw in stoppage time as Kitson and Sonko headed at Guzan but the biggest chance came to Nugent who raced through on goal but was denied as his shot was blocked by the onrushing American 'keeper.
This defeat would have ended any faint hopes that any optimistic Pompey fan had of bouncing straight back to the Premier League and now we'll be looking over our shoulder as Portsmouth currently lie in 18th place in the Championship, just five points from the relegation zone.
Steve Cotterill had a reputation for his sides being very well organised at the back but his time at Portsmouth has destroyed that reputation. Pompey have conceded nine goals in the last three games and seem to be caught out by any opposition player that has pace.
There is also the fact that the players are not quick enough to close down the opposition since Michael Brown has been missing from the side. It just shows you how big of a loss he is to the team.
You could also blame wayward finishing for today's defeat and I have to say, Dave Kitson has not performed as I would have expected this season. He missed a great chance today and doesn't seem to be much of a goalthreat overall.
The same could be said for John Utaka who can tear fullbacks apart with his pace but he lacks a good cross and his finishing is poor too. Perhaps the pair of them need some extra shooting practice?
Our next league game is a very tough trip to Nottingham Forest but before that is an FA Cup tie with the best that League One has to offer.
However, if these worrying trends in Pompey's play continue then there will be some concern that we might just discover what League One has to offer on a regular basis.
Pompey Player Ratings
Jamie Ashdown: 6 - Must hate his defence right now.
Greg Halford: 7 - Unlucky to give away the penalty but good performance overall.
Aaron Mokoena: 4 - Slow and sluggish, with little composure too.
Ricardo Rocha (Hreidarsson 25): N/A - Off with hamstring problem, I wonder if Pompey would have conceded the two second half goals if he had stayed on.
Carl Dickinson: 5 - Improved on his recent performances, but not by much.
David Nugent: 6 - Plenty of running but missed his one big chance.
Liam Lawrence: 7 - The creative difference to the side he makes is for all to see.
Hayden Mullins: 6 - Typical "no nonsense" performance.
John Utaka: 5 - Gave Solano hell but no end product at all.
Kanu: 6 - Rarely lost the ball but poses little goalthreat.
Dave Kitson: 5 - Needs to improve.
Hermann Hreidarsson (Rocha 25): 5 - Still looks off the pace.
Ibrahima Sonko (Utaka 90): N/A - Brought on as an emergency forward.
Joel Ward (Kanu 77): N/A - Wasn't really noticed.