Andy Williams's late winner saw Yeovil beat Tranmere in Gary Johnson's first home match since returning to the club.
Adam McGurk gave Rovers an early lead when he curled a 30-yard free-kick past home goalkeeper Rene Gilmartin.
Joe Edwards levelled as he fired low into the net from the edge of the area following a half-cleared corner.
Tranmere's Robbie Weir struck a post but Williams grabbed a dramatic winner in the fifth minute of injury time, heading in from Dean Parrett's cross.
VIEWS FROM THE DRESSING ROOM
Tranmere manager Les Parry told BBC Radio Merseyside:
"We've been working on defending a lot but obviously not enough and at the end of the day you can't concede two poor goals and win games.
"But it's gone now and you can't worry about things that have gone and we look at our performance and see where we can improve.
"There are a lot of positives to take out of the game, but I'm struggling to find them at the moment."