The Clarets stopped the rot after three straight defeats thanks to a late equaliser from Jamie Frost.
Frost struck five minutes from time to give Burnley a deserved reward for an impressive second-half fightback.
Tranmere went ahead after just six minutes and then led again with half an hour gone with goals either side of a smart finish from Clarets’ schoolboy Khuis Metz.
But Burnley dominated after the break and earned their point when Frost cut in and curled a superb shot in off the post to claim a first Youth Alliance point since November.
Burnley: Mitchell, Dummigan, Holt, Whitmore, Azam, Daly, Lowe, Frost, Nuttall (Bianga 76), Hill (Jackson 65), Metz (Massanka 73). Subs: Jakovlevs.