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Scunthorpe made a sensational start and deservedly took the three points following a run of four successive League defeats.
The game was only 22 seconds old when striker Andy Keogh got the better of defender Ian Sharps and planted a fine left-foot shot into the top left-hand corner from 20 yards.
Carl Tremarco was unlucky with a volley for Tranmere which just cleared the bar but generally the Merseysiders were second best in the opening period.
United doubled their lead after 39 minutes after Jason McAteer picked up a caution for a foul on Ian Barraclough.
Peter Beagrie planted the free-kick to the far post and ex-Rover Richard Hinds headed back across the face of the goal for Billy Sharp to head in from close range.
Tranmere threatened early in the second-half, but Paul Musselwhite in the visiting goal saved well from Stephen Jennings.
Tranmere made a double substitution after 55 minutes when they sent on wingers Nicky Summerbee and Sam Aiston to try and turn matters round.
Former Shrewsbury winger Aiston was unlucky to see a shot deflected over the bar and then Jennings saw an effort blocked by the outstretched leg of Musselwhite.
Michael Jackson was also out of luck with a header following a free-kick.
Keogh had a 65th minute strike disallowed for a marginal offside decision and after 77 minutes the visitors almost added a third as Matt Sparrow brought an excellent diving save from keeper John Achterberg.