Pompey were unable to stage a late comeback against table-topping Plymouth in Devon.
John Mousinho's side found themselves trailing to strikes from Sam Cosgrove and Finn Azaz.
But Reeco Hackett came off the bench to reduce the deficit and the Blues piled on plenty of late pressure.
A stoppage-time break, however, led to Ryan Hardie finding the target to condemn the visitors to a 3-1 defeat.
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