Portsmouth 3-2Â Tottenham under-21s
The Blues were much improved after the break and ensured they finished top of Southern Group D with nine points.
Andre Green returned from a two-month injury absence to score his first Pompey goal, while substitutes Gareth Evans and Oli Hawkins were also on target.
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Hide AdPhoenix Patterson and Harvey White netted for the hosts either side of the interval.
The game started at a fairly slow pace, with Green mustering the Blues' first real opportunity.
The Aston Villa loanee, making his first appearance after undergoing knee surgery in September, fired an angled right-footed shot down Spurs keeper Alfie Whiteman's throat.
The visitors took the lead two minutes later, though.
Patterson broke through on goal and his shot was blocked by the onrushing Luke McGee.
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Hide AdThe ball looped over the Blues stopper, however, with Patterson finishing into the empty net.
Jackett's side had chances to level before the break.
Ben Close should have hit the target with a 20-yard shot, while Christian Burgess' header on the stroke of half-time was well saved by Whiteman.
Pompey were much improved in the second half and equalised five minutes after the restart.
Louis Dennis' corner was headed on by Burgess, before Green turned the ball in at the far post.
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Hide AdThe Blues were the better side from thereon in and Jackett's triple substitution yielded his side's second goal.
Dennis was brought down on the edge of the box and Evans stepped up to bend a low free-kick into the bottom corner on 69 minutes.
And Hawkins wrapped up the victory for the Blues with nine minutes remaining.
Wheeler cut the ball back from the byline, with the former Dagenham & Redbridge striker stabbing home from close range.
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Hide AdWhite's left-foot free-kick in the 90th minute set up a nervy ending, yet Pompey held on and topped group D with nine points.
It means the Blues will be handed a home tie in the second round of the competition.