The striker is one of six first-team players not offered new terms by boss Paul Cook and will now depart the Latics.
Vaughan’s exit from the Championship club was widely anticipated, with the opportunity to preempt that departure and put himself in the shop window at Fratton Park failing to emerge.
The 30-year-old featured just 11 times in a disappointing Pompey loan spell during the second half of the season.
That period consisted of just two first-team starts – and no goals.
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His final appearance was as an impressive second-half substitute against Sunderland in the play-off semi-final second leg at Fratton Park earlier this month.
Vaughan had returned to the squad following a reshuffle prompted by Omar Bogle’s groin injury in the build-up.
Also released by Wigan are Callum McManaman, Darron Gibson, Jonas Olsson, Shaun MacDonald and Dan Lavercombe.
Under contract for the Latics are Pompey League two title-winning pair Gary Roberts and Kal Naismith.