It wasn’t enough to keep alive automatic promotion hopes but Pompey boss Paul Cook praised his players for showing their quality at Hartlepool.
Goals from Kal Naismith and Conor Chaplin gave the Blues a 2-0 win on Saturday.
Other results did not go in favour of Cook’s men, though.
Accrington, Oxford and Bristol Rovers all won and will fight it out on the final day for the remaining two places to go up from League Two alongside Northampton.
Pompey instead will meet Plymouth Argyle in the play-offs.
They will take confidence from a brilliant opening goal by Naismith and a classy second from Chaplin at Victoria Park.
But the performance overall was not fluent.
Cook said: ‘It was just okay, wasn’t it. It was littered with mistakes and different stuff.
‘Our quality got us home in the end. Great credit to us for that.
‘The second goal was a great goal.
‘For us the important thing is now we regroup as a club, as a team, and look to the next game.
‘We will try to see where we are with injuries and then just concentrate on the Plymouth game.’
Ahead of the final league match against Northampton at Fratton Park on Saturday, Pompey have now won six of their past eight matches as they gather momentum.
Cook is happy with the effort, although disappointed not to achieve a desired spot in the top three.
He added: ‘It’s great credit to the lads they have managed to win that many and come again.
‘We just have a tinge of disappointment because we really wanted to go up automatically and unfortunately we haven’t been able to deliver that.’