This, after Doncaster's last-gasp winner at Brentford handed Rovers the title instead.
The Cherries , already guaranteed promotion to the Championship, looked set to wrap up the title with matters goalless at Griffin Park, but a last-minute strike from James Coppinger changed everything as Bournemouth finished the campaign in second spot.
At Prenton Park Tranmere debutant Jason Mooney made a smart double save after just seven minutes to deny both Harry Arter when he fired goalwards from the edge of the box and then Shaun MacDonald on the follow-up.
The visitors started the second half brightly and almost took the lead when Arter let fly with a stunning volley which fell just wide of the upright.
Brett Pitman went even closer when he headed straight at Mooney from Marc Pugh's cross before Simon Francis rattled the stanchion with a thunderbolt on the hour - a miss which proved costly thanks to Doncaster's late winner.