Pompey eased past Crystal Palace U21s at Fratton Park to progress to the Papa John's Trophy second round.
Danny Cowley's side were leading thanks to efforts from Miguel Azeez and Gassan Ahadme as the game entered its closing stages, but that was not enough.
George Hirst then completed a 3-0 victory by scoring in stoppage-time to ensure the Blues would finish above AFC Wimbledon on goals scored.