It marks back-to-back relegations for the Merseyside club who parted company with boss Micky Adams(only took over in October) last week.
In a statement on the club website, Tranmere chairman Mark Palios said it was a "dark day in the history of Tranmere Rovers".
Palios, who became Rovers chairman in August, added: "I am desperately sorry that we were not able to avert relegation, but we can at least ensure that the club remains financially viable and returns next season ready to fight its way back into the league.
"It's devastating today but not disastrous tomorrow."
Irony of ironies former Tranmere boss Ronnie Moore - who was forced to resign over a betting incident managed to keep new club Hartlepool up at Tranmere's expense.
It also is a blot on Adams' CV - the former Port Vale boss has won promotion with four other teams and Tranmere's relegation will be a blow.