Pompey exited the Papa Johns Trophy at the quarter-final stage after slipping to a narrow defeat at Bolton.
Jón Dadi Bödvarsson netted the only goal of the game in the first half to halt the Blues’ hopes of another Wembley outing.
The Blues saw plenty of the ball in and around their opponents’ box, but did not do enough to really threaten an equaliser.
Simon Bassey made five changes from the side narrowly beaten at Tottenham in the FA Cup at the weekend.
Marlon Pack’s was recalled as the midfielder’s suspension does not apply to games in the Papa Johns Trophy.
There were also returns for Dane Scarlett, Joe Pigott, Josh Koroma and Ronan Curtis in the forward positions.
Ryan Tunnicliffe, Reeco Hackett and Colby Bishop all dropped to the bench, while Michael Morrison and Owen Dale missed out completely.
Pompey arguably had the better of the overall play during the first half and yet they were unable to properly test James Trafford between the sticks.
The keeper made a comfortable save from Koroma’s long-range effort after Ronan Curtis had seen a shot blocked.
But it was the home side who broke the deadlock on 17 minutes after breaking up the pitch from a Blues throw.
Zak Swanson’s attempted clearance was intercepted by Dion Charles and he sent Bödvarsson racing clean through to find the net.
There was lots of bright play in the centre of the pitch from the visitors, with Pack and Joe Morrell both looking bright.
But the action was quickly halted in the final third, while Swanson had to dive in to block Elias Kachunga’s attempt at the other end.
Pompey won a series of free-kicks as the half drew to a conclusion, but none of them caused the hosts much alarm.
And they might have fallen further behind just before the break, with Sean Raggett flinging himself in the path of Owen Beck’s strike to divert the ball over the bar.
Half Time: Bolton 1 Pompey 0
The visitors looked to show some fight when the action restarted, as Curtis and Scarlett both used their strength to win possession in dangerous areas.
Clear-cut chances were still proving difficult to come by for the Blues, however, despite seeing a lot of the ball.
Pigott did meet a low centre from Koroma to get a shot away, but the ball flew straight towards a grateful Trafford.
Bassey made a triple switch just past the hour mark, with Swanson, Morrell and Koroma making way for Kieron Freeman, Louis Thompson and Michael Jacobs.
It was Bolton who were next to go close, however, as Josh Griffiths prevented Randell Williams’ angled effort from drifting in, with Raggett nodding the loose ball behind.
Two more changes soon followed, as Pigott and Scarlett made way for Bishop and Hackett on 72 minutes.
Again Wanderers threatened and this time Griffiths brilliantly clawed the ball clear when Amadou Bakayoko tried to slide it into the net.
Pompey tried to hit back at the other end, but Bishop lifted a shot over with Trafford left stranded before Denver Hume saw his effort blocked.
And their best chance to force a penalty shoot-out arrived at the death, when Hackett escaped down the right and cut inside before drawing a smart stop from Trafford.
Bolton (3-4-1-2): Trafford; Toal, Santos (c), Johnston; Sadlier (Bradley 63), Williams, Sheehan (Dempsey 74), Beck (Williams 63); Kachunga; Charles (Bakayoko 74), Bödvarsson (Morley 78)
Goals: Bödvarsson 17
Booked: Johnston
Subs not used: Aimson, Lee
Pompey (4-2-3-1): Griffiths; Swanson (Freeman 64), Raggett (c), Ogilvie, Hume; Pack, Morrell (Thompson 64); Curtis, Koroma (Jacobs 64), Scarlett (Hackett 72); Pigott (Bishop 72)
Booked: Curtis
Subs not used: Oluwayemi, Tunnicliffe
Referee: Robert Madden
Attendance: 4,413 (304 Pompey fans)