Pompey exited the Bristol Street Motors Trophy after being beaten 5-2 by AFC Wimbledon in the round of 32.
A much-changed side were punished for some sloppy play by their League Two opponents at Fratton Park.
Aron Sasu, Josh Davison and Alex Pearce all struck before Kusini Yengi reduced the deficit just before the break.
Harry Pell then netted a fourth for the Dons following the restart and although Gavin Whyte grabbed his first Blues goal, Ali Al-Hamadi wrapped things up for the visitors late on.
John Mousinho made nine changes from the side that extended their advantage at the League One summit by winning at Shrewsbury on Saturday.
Yengi and Joe Rafferty were the only players to retain their place, with the latter fielded in an unfamiliar centre-back role and wearing the captain’s armband.
Josh Martin, Christian Saydee and Whyte were all handed attacking roles, while Ben Stevenson and Terry Devlin occupied the engine room.
The defence was completed by Zak Swanson, Ryley Towler and Denver Hume, in front of keeper Ryan Schofield.
Koby Mottoh and Harry Jewitt-White were both named on an otherwise experienced bench that included leading marksman Colby Bishop.
It was, to be blunt, a first half to forget for the hosts, who looked vulnerable at the back – which their opponents were quick to capitalise on.
Pearce had already nodded a James Tilley corner over the bar when they broke the deadlock on 11 minutes.
Sasu caught Devlin in possession and advanced forward before bending in a shot that Schofield could not keep out.
It almost got worse a few minutes later, as Charlie Lakin stole the ball from Stevenson, only for the midfielder to shoot wastefully wide.
But the Dons did double their advantage midway through the half after Devlin had lost the ball again, this time to Lakin.
He slotted a long pass through to Davison, who raced clear to slot the ball home and leave Fratton Park stunned.
AFC Wimbledon were not done there, though, and when Schofield failed to collect a Tilley corner, Pearce fired home.
But the keeper was at his best moments later, getting down low to his left to smartly keep out Tilley’s effort.
Pompey finally started to regain their composure as the interval approached and referee Craig Hicks played a smart advantage after Saydee had been fouled.
Devlin collected the ball and slipped a neat pass through to Yengi, whose low shot was cleared from the line by former Blues defender Lee Brown.
But YENGI did provide the hosts with a lifeline on 43 minutes, getting on the end of Hume’s cross to head into the net.
Half Time: Pompey 1 AFC Wimbledon 3
There was a change at the break, with Yengi making way and the fit-again Anthony Scully enjoying a welcome return.
But hopes of a fightback were dealt a blow when the Dons restored their advantage within three minutes of the restart.
Rafferty was penalised for fouling Sasu on the edge of the box and Pell’s low free-kick went straight through the wall and into the net.
Pompey kept fighting, however, and found another goal when Devlin caught Ryan Johnson dithering and cut the ball back for WHYTE to fire home and open his account for the club.
They had suddenly found a new gear and were starting to attack their opponents with menace, roared on by an enlivened crowd.
The Dons then almost took advantage of a fortunate bounce at the other end of the pitch, but Schofield did well to deny Davison.
Mousinho brought on some fresh legs on 68 minutes, with young Jewitt-White replacing Swanson at right-back.
They were still causing the visitors some problems, but the final ball to test Nik Tzanev was not quite there.
Two more attacking changes followed, as Bishop and Mottoh were brought on for Rafferty and Martin.
But the Blues could not score again and it was AFC Wimbledon who had the final say when Josh Neufville squared for fellow substitute Al-Hamadi to net from a few yards out.
Pompey (4-2-3-1): Schofield; Swanson (Jewitt-White 68), Rafferty (c) (Bishop 79), Towler, Hume; Devlin, Stevenson; Whyte, Saydee, Martin (Mottoh 79); Yengi (Scully 46)
Goals: Yengi 43, Whyte 58
Booked: Rafferty, Hume, Towler
Subs not used: Norris, Sparkes, Kamara
AFC Wimbledon (4-4-2): Tzanev; Ogundere, Pearce (c), Johnson, Brown; Tilley (Reeves 69), Lakin, Ball, Sasu (Neufville 75); Davison (Al-Hamadi 75 (Biler 90+7)), Pell (Bugiel 75)
Goals: Sasu 11, Davison 22, Pearce 28, Pell 48, Al-Hamadi 89
Booked: Johnson, Pearce, Tilley
Subs not used: Bass, Currie
Referee: Craig Hicks
Attendance: 7,922 (186 away fans)