Pompey will meet Sunderland in the play-off semi-finals after finishing fourth in League One following a 1-1 draw with Accrington.
Kenny Jackett’s men slipped a place in the table on the final day of the season, finishing behind Charlton on goal difference.
The Blues had to fight from a goal down against Stanley, with Ben Close cancelling out Sean McConville’s opener.
Accrington went agonisingly close to opening the scoring in the eighth minute when Anton Walkes completely lost Sean McConville at the back post, but he headed Janoi’s Donacien’s cross against the bar.
Ben Close had the Blues’ first sight of goal but his shot rolled harmlessly into the arms of former Fratton Park triallist Dimitar Evtimov.
In the 27th minute home keeper Craig MacGillivray had to be alert to keep out Paul Smyth’s shot at the near post.
And it was Pompey who should have taken the lead seven minutes later. Gareth Evans’ free-kick picked out Christian Burgess at the back post but he glanced wide.
It was then Oli Hawkins’ turn to miss a good opportunity on 41 minutes when he headed Lee Brown’s cross over.
Two minutes before half-time Bryn Morris fired a shot well over the bar when in a decent position.
Stanley shell-shocked Jackett’s men by breaking the deadlock just 44 seconds into the second period.
Tom Naylor lost possession in the middle of the park, with McConville driving towards goal before cracking a right-footed shot from the edge of the box which found the bottom corner.
Pompey’s reaction was a good one, though, with Ronan Curtis putting in a teasing cross but Oli Hawkins had the ball taken off his boot by a visiting defender.
Burgess then missed a second big opportunity in the 57th minute when he nodded Gareth Evans’ cross wide.
But the equaliser did arrive for Pompey two minutes later. Close and Hawkins played a neat one-two before the former caught Evitmov out at his near post and drilled home.
McConville almost grabbed his second of the game on 73 minutes but his free-kick went narrowly wide of MacGillivray’s left-hand post.
In the 80th minute, Close thought he’d put the Blues ahead when his 25-yard rocket had Evtimov beaten but the ball crashed off the woodwork.
The home side pushed for an equaliser but couldn’t really test Evtimov in the closing stages.
With Charlton defeating Rochdale 4-0, it meant they leapfrogged Pompey into third on goal difference.
It means Pompey will play Sunderland five times this season. The play-off semi-final first leg takes place at the Stadium of Light on Saturday, May 11 (7.30pm).