The game was overshadowed by the arrival of Joe Pigott from Ipswich on Friday night, while Marcus Harness departed the other way.
And the Tractor Boys’ loanee went straight into the starting line-up along with West Brom stopper Josh Griffiths, who arrived earlier in the week on a season-long loan.
The duo were joined by summer acquisitions, Marlon Pack, Zak Swanson and Joe Rafferty in a strong Pompey side.
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Reeco Hackett netted his first goal of pre-season in the first half before a bizarre Olly Lee corner found its way into the net, before Connor Ogilvie headed home a late winner in the last minute.
It was the hosts who started the better of the two sides with Harris’ side looking the most lively when on the ball.
Gills left-back David Tutonda thought he caught Griffiths napping in the early stages with an optimistic shot on the halfway line, but his effort didn’t trouble the Pompey keeper.
The visitors slowly grew into the game and it took just 15 minutes for Pigott to have his first attempt on goal with a hopeful volley. However, he fired his shot high and wide of the goal.
Two minutes later, there were strong claims for a Pompey penalty when Michael Jacobs collided with former Blues midfielder Stuart O’Keefe, but referee Tim Robinson waived those appeals away.
After a dominant spell in possession, Cowley’s side took the lead on 27 minutes when Jacobs put Reeco Hackett, who placed the ball into Jake Turner’s net.
And it was more of the same, with the Blues happy bring up their possession stats, frustrating the Gills in the warm summer heat at Priestfield.
After 35 minutes, Ronan Curtis found himself in behind the host’s backline and tried an audacious chip over Turner but his lob didn’t worry the stopper.
The hosts in fact ended the first half the more stronger side causing some trouble to the Blues’ backline.
And Pompey came out looking strong again despite a number of stoppages in the earlier proceedings of the second period.
After 54 minutes, a good run forward by Rafferty saw Jacobs, Curtis and Pigott combining on the edge of the box before the Ipswich loanee unleashed a shot on target.
Cowley continued to ring the changes on 64 minutes which brought to an end Griffiths and Pigott’s first Pompey appearances.
Straight after coming on, Toby Stewart was called into action making three amazing saves to keep the tie level.
But his efforts were undone on 70 minutes with the resulting corner finding it’s way into the net with the goal being awarded to Olly Lee.
It was a much younger Pompey side that finished the game but continued with the same intensity and they found a late winner with Connor Ogilvie heading home a late winner against his former club in the 90th minute.