Pompey had been finishing the season with a flourish, despite missing out on a League One play-off spot.
But they tripped over the final hurdle, slipping to a 4-1 defeat at a Sheffield Wednesday outfit who did secure their top six spot.
George Hirst had given the visitors an early advantage, but Lee Gregory, Saido Berahino, Jordan Storey and George Byers secured an Owls turnaround.
And Danny Cowley was disappointed with the manner of the goals that his side conceded at Hillsborough.
The Blues boss: “I thought we had control in the first 20 minutes after taking the lead, but I have to credit Sheffield Wednesday, who are a top team at this level.
“Their pace, athleticism and power is the best in the division and they were able to get momentum after levelling.
"We weren’t clinical or ruthless enough to take them and then let in a fourth goal that was just unacceptable for us because people weren’t doing their jobs properly."
“But we have conceded three goals from set-pieces after finding a really good way into the game, which is frustrating.
“We found it difficult, although then did quite well when we came out for the second half and created a number of chances.
“But we weren’t clinical or ruthless enough to take them and then let in a fourth goal that was just unacceptable for us because people weren’t doing their jobs properly.”
The campaign might now be over, but Cowley is not ready to put his feet up and relax on a sun lounger.
He said: “I’ll be back in first thing tomorrow to work and we sit down with all the players to do a performance review.
“It’s an opportunity for us to help and support them in their development, as well as to receive some feedback.
“There will be players who move on now – whether they’ve been on loan or not. It’s the natural evolution of a team.”