Substitute Gareth Evans, Brett Pitman, Lee Brown, Jamal Lowe and Oli Hawkins netted from the spot as the Blues won 5-4 in the shoot-out after it finished 2-2 after extra-time.
Here’s chief sports writer Neil Allen’s Pompey player ratings
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The keeper who prides himself on his penalty record made one stop and that was all it took to give Blues the advantage and win the cup - 8
Photo: Bryn Lennon
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What a time to score your first Pompey goal, his late header sending the match into extra time. Recovered from a difficult opening 45 minutes to produce a typical dogged defensive display - 8
Photo: Joe Pepler
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Appeared in every Checkatrade Trophy match for Pompey this season and deservedly now a winner. Put his body on the line and shone during some tough early moments for the Blues - 8
Photo: Joe Pepler
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Another who helped his team somehow stagger to half-time with damage limitation, the centre-half grew stronger as the game wore on and played a pivotal role in the build-up to Thompson’s equaliser - 8
Photo: Joe Pepler