A 1-2 defeat at home to Bradford City saw Tranmere relegated to League 2.
Rovers took the lead through Matthew Pennington but had to play the final hour with ten men following the sending off of Junior Brown.
Two second half goals gave the Bantams the win, while results elsewhere meant Rovers would have gone down even had they picked up all three points.
There were three changes to the team that started at Leyton Orient as Ian Goodison and Jason Koumas returned from injury to take the places of Danny Holmes and Jake Cassidy, while Jason Mooney came in for his third start of the season in place of the injured Owain Fon Williams.
Bradford started brightly, winning a corner in the first minute after Mooney turned a long range effort from Aaron McLean around the post, and the Rovers keeper saved soon after from Nathan Doyle.
However, Rovers responded well. After a spell of possession deep in the Bradford half, Matthew Pennington picked up a loose ball, ran into the Bradford area and lifted a shot over Jon McLaughlin which the keeper let through his hands and into the net.
Mooney had to save from McLean within a minute of the goal and Tranmere then survived a scramble with Pennington and Max Power getting vital headers in.
Power forced a good one handed save out of McLaughlin on 19 minutes with a looping header from Liam Ridehalgh's left wing cross, while Mooney breathed a sigh of relief at the other end after a cross from Garry Thompson went over him and only just past the far post.
Players and staff from both teas got involved in a scuffle in front of the Bradford dugout around the 25 minute mark and five minutes later Rovers were reduced to ten men when Junior Brown was shown a straight red card for a late challenge on Nathan Doyle.
With a man disadvantage Rovers switched to 4-4-1, with Akpa Akpro moving to a wide left role. On 31 minutes he played Power into the area and the midfielder skipped past Doyle but his pass for Ryan Lowe was cleared by a defender.
Stead fired wide from the edge of the area in first half added time and volleyed over at the back post two minutes into the second half.
With a man advantage Bradford were dominating the possession and spending much of the time inside the Tranmere half. Adam Drury drilled a back post volley over the Tranmere goal on 54 minutes.
Though Crewe were 2-0 up against Preston, a goal for Oldham against Notts County briefly lifted Rovers out of the bottom four to the delight of the fans inside Prenton Park. However, less than ten minutes later County equalised from the penalty spot to put Rovers back to 21st.
Lowe went down under a challenge inside the Bradford area on 74 minutes but the referee waved away penalty appeals and seven minutes later the visitors equalised, when Stead's strike from the edge of the area deflected past Mooney and into the bottom left corner.
Rovers had a chance to regain the lead on 84 minutes when Koumas sent Akpa Akpro through on goal but the striker's attempted lob lacked power and McLaughlin gathered inside his six yard box.
And the miss seemed even more pivotal a minute later as Aaron McLean drilled a shot past Mooney from the right side of the penalty area to put the Bantams 1-2 up.
McLean was denied a second two minutes later by a fantastic block from Pennington and though Rovers threw men forward late on, they couldn't find a way back into the game.
Tranmere: Mooney, Pennington, Taylor, Goodison, Ridehalgh (Kirby 89), Power (Rowe 89), Koumas, Jennings, Brown, Akpa Akpro, Lowe. Unused substitutes: Ramsbottom, Holmes, Arthurworrey, Baggie, Stockton.
Bradford: McLaughlin, Darby, McArdle, Davies, Drury (Meredith 59), Thompson (Bennett 59), Doyle (De Vita 64), Jones, Yeates, Mclean, Stead. Unused substitutes: Dolan, Jameson, McHugh, McBurnie.
Referee: Graham Scott
Yellow cards: Jones (15)
Red card: Brown (30)