A 14th away defeat of the season condemned Grimsby Town to relegation for a second successive year.
It seemed to be going well for the Mariners when they led by the only goal at half-time but defensive errors in the second half allowed Tranmere to tip the balance.
The second goal for the Merseysiders came when they were down to ten men, after Ian Sharps went off in the 59th minute for a second yellow card offence.
Grimsby nearly fell behind inside the first minute when Greg Young turned a David Beresford cross onto his own bar.
But the Mariners showed commendable spirit to sneak ahead in the 24th minute.
Isaiah Rankin, after a lively run, saw his angled shot blocked near the line but Darren Mansaram was on hand to net from close range.
Tranmere changed their formation after half-time and began to take charge. Iain Hume headed them level from a Ryan Taylor cross in the 56th minute with the ball going in off the post.
Then Hume turned provider in the 61st minute for Eugene Dadi who had gone on as a 46th minute substitute to net the winner although it seemed he was in an offside position.
Grimsby tried hard to get back in the picture but two good efforts by Jason Crowe went unrewarded and a Darren Barnard free-kick was well held by home keeper John Achterberg.
"It is a day everyone was dreading," said Grimsby boss Nicky Law. "I thought we were going to do it but in the end Tranmere were by far the better side even when down to ten men.
"It is just massively disappointing for the club, the directors and the supporters, but when you concede 81 goals in a season you are going to find it hard to stay in the division.
"It isn't about what has happened today. It is what has happened over the season." Tranmere manager Brian Little said: "It was an awkward one for us today because of the Grimsby situation, but you have just got to do your bit.
"My lads reacted well and played well but you cannot help but feel sorry for Grimsby. It is a cruel business. It is a funny sort of feeling but I have got to do my job.
"I was disappointed with the sending off decision. I cannot believe the second incident deserved a yellow card.
"Everything has gone well for me since I came here and I must try and take it on from here next season."