Hartlepool paid for failing to make the most of their chances, according to Craig Hignett.
The Pools manager felt it was Pompey who showed the extra class required when it mattered in the game.
On the balance of play he thought his side deserved to get something from the Victoria Park contest.
But second-half goals from Kal Naismith and Conor Chaplin proved the difference as the Blues won 2-0.
They were both finishes that would grace a higher level and Hignett’s side were unable to replicate the same standard with their opportunities in the game.
He said: ‘You could see Portsmouth are a good side who have a little bit of extra quality where it mattered in the final third.
‘You have to be disappointed when you see the chances we created and missed.’
Substitute Rhys Oates failed to take a couple of decent chances for Hartlepool in the second half.
He was denied by a good save from Pompey keeper Brian Murphy soon after coming on.
The striker then headed over the top when he was well positioned in the box.
According to Hignett his team had the better of the opportunities overall.
He added: ‘There were chances in the game but I think we had the better ones.
‘We counted seven in the second half and they are the fine margins.
‘Football-wise, I thought we were fine – we played some good stuff but we have to be clinical and we weren’t.’
It hasn’t been a good run of form for Hartlepool as they get set to finish their League Two campaign with a trip to Plymouth on Saturday.
But Hignett has focused on the efforts his men have put in since he took charge of the club in February.
He added: ‘I’ve thanked the players for everything they have done because they deserve a lot of credit.
‘I know we’ve lost three in a row now but what they’ve done since I’ve been at the club is fantastic.’