Pompey had to play for more than 70 minutes with just 10 men at Brisbane Road.
Sean Raggett was dismissed for bringing down Theo Archibald as the Leyton Orient forward was about to burst through on goal.
But it did not stop the visitors from winning 2-1 to secure top spot in their Bristol Street Motors Trophy group.
Abu Kamara grabbed the winner after Christian Saydee’s opener had been cancelled out by Joe Pigott.
And after sorting themselves out following the red card, John Mousinho was delighted with how his side fared.
The Blues boss said: “The most important thing for us was to make sure that we reached the next stage of the competition.
“Once we ironed out a few issues from before the break, I thought that we superb in the second half. I was pleased with the effort we showed with just 10 men.
“We’d caused ourselves some problems and got opened up in the middle of the pitch, with Raggs unfortunate enough to run across the man.
"We had a really good chance just before we went ahead and restricted Leyton Orient to very few chances."
“It probably was a red card, but that was from our own creation and we then needed to get to grips with the new shape.
“We had a really good chance just before we went ahead and restricted Leyton Orient to very few chances.
“There were lads out there who hadn’t played very much recently, so I was really pleased with how we did.”
Frustrations boiled over on the bench on a couple of occasions, with Pompey delayed in bringing on Terry Devlin before an argument led to goalkeeping coach Joe Prodomo being booked.
Mousinho said: “When Christian came off the pitch, their manager decided to use some choice language towards him and I’m not sure what the point is of that.
“He reacted and went towards him, so we dragged him away. Joe wasn’t having any of that and let Richie know what he thought, which I don’t have a problem with.
“With the substitution, the officials wouldn’t let us make the change because Leyton Orient had put the numbers down wrong on the team sheet.
“It’s totally bizarre and you can probably understand how frustrated we were because everything was fine on our end.”