Scunthorpe struck first just before half-time after Tranmere had bossed most of the early stages with the wind at their backs.
The home side's goal came after 42 minutes when Ian Morris curled a free-kick towards the far post for striker Andy Keogh to apply the finishing touch from close range.
It was Keogh's first goal for two months and seemingly put Scunthorpe into a commanding position.
Tranmere had been unable to find their finishing touch in front of goal.
Striker Chris Greenacre and winger Chris Shuker both fired in early efforts but each provided a routine save for goalkeeper Joe Murphy.
Nine minutes into the second half the visitors did at last find their touch.
A curling cross from the right by John Thompson was flicked on in the box by John Mullin for skipper Shane Sherriff to come in at the far post and force his shot past Murphy.
Five minutes later Scunthorpe were unlucky not to go back in front when a low cross from the right by Cleveland Taylor found midfield man Matt Sparrow, who turned to fire in a shot which crashed back into play off the foot of the far post.
Defender Richard Hinds was also just a whisker away from a winner for the home side with a header from a Sparrow corner.
Scunthorpe pressed forward strongly looking for all three points but 16-goal leading marksman Billy Sharp was always closely watched by a Tranmere defence in which Ian Goodison and Chris McCready were commanding figures.
Substitute Robbie Stockdale had a chance late in the game to snatch victory for the visitors but lifted his shot high over the top.
It was the first points Tranmere have dropped in five league games while Scunthorpe stretched their unbeaten run to seven games.