Leon Best scored the game's only goal on 14 minutes, tapping home at the far post after good work down the left by Fabio Nunes.
Rovers were made to work hard for the win, as they were forced to deal with a succession of set-pieces from their Portuguese hosts.
But they held out in the Alrgave heat to maintain their unbeaten start to their summer schedule.
"We said all along that the result was never going to be the most important thing, but winning football matches is a good habit to get into," said Bowyer.
"It was a really well-worked goal and on another day we could have had one or two more.
"I have to give credit to Portimonense, because they put us under a lot of pressure at times, but I thought we coped with it extremely well.
"There was a real determination and desire from the players, in each half, to keep a clean sheet and that was great to see.
"There were a few tired legs out there, which was to be expected after a tough week's training in intense heat, but I thought the lads worked hard for each other and got the fitness levels out of it that we wanted.
"A special mention must go to the new boys, who have settled in really well. DJ, Tayls and Judger all looked lively, Alex Marrow put himself about in midfield, Killa was very solid at the back and Simon Eastwood made a great save late on.
"I also want to say a huge thank you to the 100 or so fans who made the long journey out to Portugal for the game. Your vocal support was greatly appreciated by myself and the players.
"Overall, it has been a very worthwhile trip from a fitness and training point of view. There has been a great spirit within the camp, everyone involved has worked exceptionally hard and has bought in to the way we want to do things.
"We look forward to stepping up our pre-season preparations now at Crewe on Tuesday night."
Tickets for the match at Gresty Road will be available on the evening, priced £8 Adults, £4 Seniors over 60 and £2 for Under 16s.