Pompey finished their Youth Alliance League campaign with a 3-2 defeat at Cheltenham.
But the Blues’ superior goal difference meant they secured sixth spot ahead of the Robins to qualify for Merit League One.
They took the lead when Oscar Johnston was brought down outside the box and Bradley Lethbridge (pictured) curled home the free-kick.
But Aaron Evans-Harriott, Callum Ebanks and Olly Price all netted for the Robins before the break to turn the match on its head.
And the Blues were dealt a further blow in the first half, as Liam Kelly was carried off after suffering a knee injury.
Lethbridge nodded home a second goal for the visitors following the interval, but they were unable to find a leveller.
Academy manager Mark Kelly said: “Brad scored with a free-kick and we then enjoyed a period of control, where we could have had a couple more.
“But we conceded from a ball over the top because we didn’t get our lines right and then we were unable to clear a ball and it was scrambled into the net.
"Getting into Merit League One is a nice reward for the boys’ efforts and we’re looking forward to the challenge."
“Liam was taken off after that and we just didn’t recover from it, with Cheltenham scoring a third before half-time.
“We had a little bit of a discussion at the break and came out a lot brighter, moving the ball quicker and got one back.
“It was all us from that point, but our quality was not quite right in the final third and we couldn’t dig ourselves out of the hole we’d got into it.
“The game came on the back of a long week – with the trip to Plymouth in mid-week – and we’ve had a lot of matches lately.
“Getting into Merit League One is a nice reward for the boys’ efforts and we’re looking forward to the challenge.
“But there’s a couple of weeks before that starts up. We probably need that to recoup before we’re ready to go again.”
Pompey: Durin; Kavanagh, Robb, Bruce (Rew 53), Kelly (Teggart 40); Bridgman, Whiting; Johnston, Stanley, Flint; Lethbridge