The talented 19-year-old centre-back missed out on the play-offs due to injury last season as his loan spell at Fratton Park finished in disappointing fashion.
But now he has sealed a permanent deal to return, with Adam Webster’s move in the other direction also completed.
Clarke has signed a three-year deal with the Blues as part of the deal, with Ipswich also paying an undisclosed fee for Webster.
It represents the ideal opportunity for the centre-back to banish the misery of being sidelined while Pompey lost to Plymouth over two legs.
‘This club might be in League Two, but everything’s set-up for us to be at a higher level and we want to make sure that happens,’ said Clarke, speaking to Pompey’s official club website.
‘It was devastating for me to miss the play-off games with a niggly injury after working so hard throughout the campaign.
‘But now I’m raring to get started again and am looking forward to what’s ahead at Pompey.’
Meanwhile, Webster moves up to the Championship with Ipswich after making 81 appearances for the Blues.
‘I want to thank everyone at Portsmouth who has helped me in my career,’ said Webster, speaking to the Ipswich Town website.
‘It’s a great club and I have some fantastic memories from my time there but now I can’t wait to get started as an Ipswich player.
‘It’s a big test for me, stepping up to the Championship and joining a club like Ipswich but I’m ready for the challenge and I’m looking forward to meeting the rest of the squad in pre-season.’