Kenny Jackett’s men collected two points from their final Group B fixture ensuring they secured top spot and set up a home tie in the next round.
Oxford also made it through to the knockout stages following the draw with Pompey, although they cannot finish top of the group.
The U’s still have a game against Crawley to come in the competition, but the Blues sit four points above them in top spot.
'We wanted to show him a bit of love' - Portsmouth-based Spurs fans' terrific gesture to ensure Dane Scarlett feels at home on the south-coast
Ronan Curtis' Portsmouth future spelt out by trusted source well in the know - with advice on where to play Irishman added, too
League One latest: Portsmouth linked duo set for Oxford United and Lincoln moves, Southampton prospect joins Blues rivals as Ipswich land former Blackpool and Derby veteran
Portsmouth's Miniesta bidding to live up to big reputation - and those comparisons with ex-Barcelona and Spain star
The most expensive estimated League One combined XI - including two Portsmouth, four Barnsley, one Oxford United and two Derby aces
Oxford manager Karl Robinson was ultimately disappointed his side missed out on winning Group B.
And the U’s boss highlighted his team’s failure to make the most of the ‘good positions’ they found themselves as a key to not overcoming Pompey.
Robinson told the Oxford Mail: ‘We wanted to finish top of the group, so it’s disappointing.
‘I think we would have felt worse if we weren’t creating the chances.
‘We were getting in good positions so to not finish it off is frustrating. I think it was apparent that was our problem.’
But Robinson was pleased with the fact Oxford secured their progress with a game to spare, joining Pompey in the knockout stages.
The Oxford boss revealed he will now go with a youthful line up in the final group match at Crawley next month, give that qualification has now been secured.
He added: ‘The objective when you come into these competitions is to qualify from the group and if you can do it in the first two games it’s brilliant.
‘We can now play a really young team at Crawley.
‘I’m really pleased we showed a bit of fight towards the end to not lose the game, because it could have been so different if we hadn’t got that goal.’