The Pompey boss named two changes to his first half XI as triallist Josh Gould replaced Alex Bass in goal, while Michael Jacobs made his first pre-season outing - replacing Louis Thompson in midfield.
Bournemouth striker Christian Saydee continued to lead the line and had the best chance of the first half which he fired wide.
The visitors fell behind after 13 minutes as Bradley Tarbuck forced a mistake in the Blues’ midfield which freed Andreas Robinson, who calmly placed the only goal of the game.
Like Saturday’s fixture against the Hawks, Cowley made 11 changes which included triallists, Andre Wisdom, Levi Andoh and Rumarn Burrell, while 17-year-old Toby Stewart was trusted in goal.
There was no Marlon Pack, who continued to remain absent from this weekend's fixtures along with Denver Hume and Reeco Hackett.
Pompey started the opening stages as the more dominant side with Marcus Harness and Ronan Curtis unleashing their pace on the flanks to open up the Borough defence.
After nine minutes, the former Burton winger had the ball in the back of the net for the visitors, but he was judged to be offside.
Less than five minutes later though, Cowley’s side fell behind following good pressure from Bradley Tarbuck with Andreas Robinson firing the hosts into the lead.
The Blues’ best chance of the half fell to Saydee but, despite doing all the ward work, fired his shot wide from five-yards-out.
Pompey continued to knock on the door with Curtis finding space but he dragged his effort wide of the target on the half-an-hour mark.
But that was good as it got for Cowley’s side in the first 45 with Gosport ending the first period the much better side.
After making 11 changes at the break, the now much youthful Blues shot out of the blocks, showing much more promise in finding a leveller.
Jayden Reid was Pompey’s brightest spark with his pace and skill causing plenty of trouble to the Borough backline.
And it was the former Birmingham man who was gifted with a glorious opportunity to level the friendly in the early stages of the second half but his effort was fired over the bar.
Jay Mingi continued to impress in the centre of midfield following his standout performance against the Hawks on Saturday.
The Blues continued to pile on the pressure with Harry Jewitt-White and Alfie Bridgman coming closest with long distance attempts.
But the youthful Pompey squad couldn’t find the back of the net despite plenty of pressure on the Gosport goal.
In the 88th minute, Reid had one of the best chances of the friendly but somehow managed to blaze his shot over, capping off a tough afternoon at Privett Park.