It was bitter disappointment for Tranmere in a first defeat in nine outings.
Two clubs in the thick of the League One promotion race engaged in a tense battle at Prenton Park.
Doncaster could not have wished for a better start. James Coppinger was allowed to advance to the edge of the box in the second minute from a mistake by Anthony Kay before beating Danny Coyne with a well-flighted effort into the top corner.
They could easily have doubled their margin a few minutes later with ex-Rover Jason Price wasting a good chance.
But the Merseysiders gradually warmed to their task and a Jennison Myrie-Williams shot was deflected for a corner from which Kay headed just outside a post.
Then John Mullin and Ian Moore were only just off target after good approach work.
Coppinger was always busy in the Doncaster five-man midfield and tested Coyne with a low drive on 36 minutes.
Brian Stock collected the only first-half caution for a foul on Kay in a game in which no quarter was given.
Chris Greenacre had no luck with a couple of overhead efforts for Tranmere soon after the re-start and the Yorkshire side remained dogged in defence with Steve Roberts well to the fore.
There was a blow for the visitors when Price was helped off with a leg injury after 52 minutes with Stuart Elliott going on.
Tranmere were becoming a little frustrated and were not helped when Paul McLaren blazed over after a throw in approaching the hour.
They kept battling away with Kay, Moore and McLaren putting in a sound contribution.
It became a real backs-to-the wall task for Doncaster, but they stood firm with Neil Sullivan making an important late stop from a Moore header.