Mark McChrystal put Rovers into a half-time lead but Garry Thompson ensured the shares were spoiled between two sides safe in the lower reaches of League One.
Jake Cassidy was inches off target for Tranmere following a third-minute corner, while at the other end Owain Fon Williams made a fine fingertip save to deny Niall Canavan.
The hosts opened the scoring after 27 minutes, with McChrystal heading in from an Andy Robinson corner.
Bobby Grant enjoyed no luck with two good attempts as the visitors tried to get back on terms before the break.
Martin Devaney found the side-netting after an excellent Tranmere move just short of the hour mark but Scunthorpe equalised soon after, Thompson producing an excellent finish after Mark Duffy's corner was only part cleared. And the Iron went close to a 70th-minute winner when Eddie Nolan struck the top of the crossbar.
