The night Ivan Toney inflicted terrible damage on Portsmouth
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It was the penultimate match of the season for both teams with Pompey needing to win to step into the automatic promotion places and Posh requiring three points to keep alive their hopes of a play-off finish.
Posh roared into a 2-0 lead in the first half an hour with goals from Lee Tomlin and Ivan Toney, but the hosts were level early in the second half with former Posh defender Christian Burgess claiming the equaliser.
But Toney grabbed the 75th-minute winner which deflated the majority of the 18,500 crowd.
Posh: Chapman, Naismith, Tafazolli, White, Knight, Lafferty, Woodyard, Ward, Maddison, Toney, Tomlin. Sub used: Dembele.
Posh went on to win their final League One game, but still missed out on the play-offs by a point.
Portsmouth went on to lose their play-off semi-final with Sunderland.
Posh have won four and lost five of their 12 Football League games at Portsmouth.
Their previous win had arrived in September, 2011 when a last-minute own goal secured another 3-2 Posh win after midfielder Lee Frecklington had scored twice in the first quarter of the match.
Last season Jack Marriott gave Posh a fifth minute lead, but two goals from on-loan Spurs forward Dane Scarlett secured a 2-1 Pompey win.