Brett Pitman took his tally to the season to 25 with both goals to see the Blues finish eighth in League One.
Alex Bass kept a clean sheet as he was handed his first league appearance from Kenny Jackett.
And Matt Clarke was rewarded for outstanding form as he was named The News-Sports Mail player of the season before kick-off.
It's no exaggeration to say Pitman could have bagged five goals in the first 45 minutes, which would have given him real hope of landing the golden boot.
He beat Liam Shephard in the eighth minute and went clear but Jonathan Bond was equal to his finish.
The goal arrived in the 13th minute as the striker headed in Gareth Evans' corner at the near post.
The second came after 25 minutes as Pitman got the touch at the back post and turned in Lowe's effort across the face of goal.
There was an amusing moment as the PA gave the goal to Lowe, only to be given a volley of abuse from the captain before correcting his error.
Pitman then somehow blazed over from three yards out after getting on the end of Clarke's backheel in the 33rd minute.
There was still time for Pitman to extend Bond into a full-length stop three minutes before the break from his angled 20 yarder.
The second half proved to be a sleepy affair with little noteworthy action for most of the half.
Kal Naismith was given a standing ovation when replaced by Matt Kennedy on what could be his final Pompey appearance.
And Pitman headed at Bond with 12 minutes remaining after Evans' free-kick was played back in by Stuart O'Keefe.
The players returned to the pitch after the final whistle for a lap of appreciation with Fratton Park in upbeat mood at the season's close.