Grant Hanley's 11th minute header was the only goal of the game at Gresty Road, powering home Ruben Rochina's inswinging corner.
Against a lively Crewe side Rovers had to work hard with the majority of the players getting 70 minutes under their belts in humid conditions to maintain their unbeaten pre-season record.
"I've said all along, it is about the fitness levels," said Bowyer post-match.
"We knew we would be coming into the game heavy legged and it showed at times, but the most important thing was that they got their 70 minutes in the bank. It is all detailed preparation and we are delighted.
"We've had two teams play today, we had a game this morning where those who played got 70 minutes and the game tonight where they got 70 minutes which was the plan.
"We are cranking it up a little in terms of the game on Saturday against Rochdale, so everything is going according to plan in terms of the fitness levels, the performances need to improve that is for sure and we are working hard at that.
"It is always nice to win, but like I've said before, in pre-season it is about getting good habits and getting the fitness levels higher and we've achieved that tonight, we've seen the data and we are pleased with what they've scored in terms of their fitness levels."
Crewe provided testing opposition at times with goalkeepers Jake Kean and substitute Matty Urwin having to make crucial saves to ensure a second consecutive clean sheet following the 1-0 win over Portimonense at the weekend.
"I've just said in the dressing room that it is a good habit to keep a clean sheet and it is a good habit to win even though pre-season isn't about winning," added the Rovers boss.
"I can't knock the lads for their effort over the last ten days, it has been a real tough ten days and coming off the back of a long trip I'm delighted with their efforts since they've come back."
Rovers are back in pre-season action this Saturday when they travel to Spotland to take on Rochdale. Tickets are currently on sale priced £10 for Adults/Seniors and £5 for Juniors aged 16 and under.