Pompey progressed to the Papa Johns Trophy knockout stages, despite being held to a draw by AFC Wimbledon at Fratton Park.
They knew beforehand that one point would be enough to go through, but were on course for top spot when Ronan Curtis fired them ahead.
Ultimately, though, they had to settle for the runners-up position in Southern Group B, with Ayoub Assal levelling for the Dons after the break.
The resulting penalty shoot-out decided nothing, but Josh Oluwayemi made three saves to ensure it was the Blues who claimed a bonus point.
Danny Cowley made seven changes from the side that drew with Shrewsbury in the league at the weekend.
Zak Swanson, Owen Dale, Ryan Tunnicliffe and Dane Scarlett were the only players to keep their spot in the starting line-up.
Oluwayemi returned between the sticks, while Denver Hume, Kieron Freeman and Michael Morrison all entered the defence, the latter wearing the captain’s armband.
There were outings for Joe Morrell and Curtis in midfield, with Joe Pigott given a chance to impress up front.
Academy players Josh Dockerill and Malachi Osei-Owusu were both named on the bench and joined by Harry Jewitt-White following his loan spell with Gosport.
The first half was an open affair, played in strong winds and driving rain that made life difficult for both sides at times.
It was the hosts who were first to threaten and the towering Kyle Hudlin – Britain’s tallest outfield player – was well placed to nod clear when Dale’s corner was flicked towards goal by Pigott.
The danger was not over for the visitors, though, and Scarlett’s effort was scrambled behind in a packed area.
Assal then whipped in a cross at the other end that was caught by the wind and drifted narrowly over the bar.
But it was the Blues who broke the deadlock on 15 minutes after Kwaku Frimpong had made a mess of dealing with Swanson’s cross.
Scarlett’s shot was saved by Nathan Broome, but the ball landed kindly for CURTIS, who took a couple of touches before slotting home.
The tempo began to slow after that, but picked up again towards the end of the half, with both sides creating openings.
Oluwayemi had to get down quickly to his left to deal with Huseyin Biler’s long-range effort, while Broome then stuck out a leg to divert Tunnicliffe’s effort wide.
A couple of dangerous Hume deliveries also caused difficulties for the Dons, but they saw out the closing stages to go in for the break with just a one-goal deficit.
Half Time: Pompey 1 AFC Wimbledon 0
There were a couple of changes at the break, with Morrell and Swanson replaced by Jay Mingi and Connor Ogilvie.
But Pompey soon found their lead wiped out after Freeman misjudged a long Broome clearance, allowing Assal to collect the ball and bend home a neat finish.
Freeman made up for that moments later, though, by clearing Isaac Ogundere’s effort off the line after the Dons skipper had met Alfie Bendle’s corner.
A triple substitution followed for the hosts on the hour mark, with Josh Koroma, Reeco Hackett and teenage debutant Dockerill brought on for Curtis, Tunnicliffe and Morrison.
Pompey were trying to fight back, but Scarlett could only nod wide from a Dale delivery, while Hackett sent a shot over.
The game was getting stretched as the hosts looked to get forward and their opponents tried to catch them on the break.
But there was no late drama and the final whistle confirmed that the Blues had secured second spot in their group.
A shoot-out was still required to decide the destination of a bonus point, however, and Oluwayemi took centre stage.
He kept out penalties from Frimpong, Courtney Senior and Aron Sasu, while Koroma, Hackett and Scarlett all scored to end the evening on a high.
Pompey (4-4-2): Oluwayemi; Swanson (Ogilvie 46), Morrison (c) (Dockerill 60), Freeman, Hume; Dale, Tunnicliffe (Hackett 60), Morrell (Mingi 46), Curtis (Koroma 60); Scarlett, Pigott
Goals: Curtis 15
Subs not used: Osei-Owusu, Jewitt-White
AFC Wimbledon (4-4-2): Broome; Frimpong, Jenkins (Towler 81), Ogundere (c), Biler; Senior, Bendle, Maghoma (Woodyard 73), Assal (Currie 73); Bartley (Sasu 81), Hudlin
Goals: Assal 50
Booked: Biler, Bendle
Subs not used: Tzanev, Williams, Davison
Referee: Craig Hicks
Attendance: 2,545 (124 away fans)