It was also a miserable end to the season for Tranmere under caretaker manager Jason McAteer as they suffered an eighth home reverse.
Doncaster always looked the better outfit. They took a 12th minute lead through Lewis Guy when he netted with a superb shot from an acute angle after being set up by Neil Roberts.
Delroy Facey shaved the outside of a post for Tranmere and skipper Mike Jackson had a goal disallowed in the 15th minute for a push on keeper Alan Blayney.
Doncaster were gifted their second goal in the 43rd minute. Goalkeeper Steve Wilson in trying to find Carl Tremarco merely handed the ball to Guy who crossed for Roberts to head into the unguarded goal.
Only moments earlier Roberts had been denied by a spectacular one handed save by Wilson.
McAteer went on for Tranmere in the second period by they could not make an impact in front of goal.
Steve Jennings was wide after a free-kick and Chris Greenacre headed off target when set up by Gareth Roberts.
Guy missed a sitter for Doncaster following a mistake by Paul Linwood and Craig Nelthorpe should have done better with a header when set up by Sean Thornton on the hour.