There was little goalmouth action at either end before Doncaster skipper Rob Jones grabbed the all-important goal in the 63rd minute when he fired home after centre-back partner Jamie McCombe had headed down a free-kick from David Cotterill.
Doncaster always had the edge in a hard fought clash and just about deserved to grind down their opponents.
The victory put Doncaster seven points clear of third place, but Flynn said: "We haven't set a points target and I've no idea how many more we need to win.
"The games are a grind at this stage of the season, but we just need to stay consistent and keep our form going and we'll get there.
"The lads put in a tough shift and had to against a good Tranmere team who never stopped trying to get back at us.
"But over the 90 minutes our keeper never had a shot to save and that's an important factor because we defend really well.
"We were up against a decent side, but I thought we largely controlled the game and I always thought one goal would be enough - even before the kick off.
"Another win next Tuesday night against Carlisle will put us on our way, but nothing's easy at this stage of the season.
"We just want to get to the last match and make sure we win promotion to reward our fans."