Kenny Jackett slammed his side for a lack of energy in their defeat at Bury.
Pompey went into the Gigg Lane encounter with a place in the play-offs still a slim possibility, only to suffer a 1-0 loss.
Shakers striker George Miller grabbed the only goal during the second half after stealing the ball from Luke McGee.
Wins elsewhere for Charlton and Scunthorpe meant the result was academic, although Jackett was still disappointed with his side’s display.
The Blues boss said: “The goal was a mistake from Luke’s point of view. It’s the wrong pitch to take chances on and that was the key moment in the game.
“It’s frustrating because we looked in pole position, but could not find the combinations to create clear-cut chances.
"We do seem to be running on empty a bit at the moment and have looked quite laboured on the ball."
“We had a lot of the ball and were on top really, getting into Bury’s half pretty quickly, although we didn’t create enough when we got there.
“Their back four weren’t really tested and I felt that we let them off because we had too many people who looked like they were lacking in energy and form.
“As much as I’ve spoken about finishing the season strongly, we’ve been poor in recent weeks and that was the case in both boxes at Bury.
“There were some brave headers and a great save from their keeper towards the end, although it wasn’t enough for us.
“We do seem to be running on empty a bit at the moment and have looked quite laboured on the ball.”
There was better news for one of Pompey’s neighbours, as Havant & Waterlooville beat Concord Rangers to secure the National League South title.
Jackett said: “Congratulations to them all because it’s good to see a local club reach that level. Well done to Lee Bradbury and everyone there.”