Paddy Madden put Yeovil ahead after nine minutes and Sam Foley made it two just before the half-hour mark.
But James Wallace pulled one back on the stroke of half-time and Jake Cassidy equalised six minutes into the second half.
Rovers got another boost when their opponents had Joe Edwards sent off 17 minutes from time and they made the extra man count as Danny Holmes got the winner five minutes later.
The win extended Tranmere's lead at the top to seven points after their two nearest rivals both slipped up.
Stevenage stayed second, despite a 1-0 loss at Colchester, Sanchez Watt with the 55th-minute winner, two minutes after the visitors had Anthony Grant sent off.
Sheffield United conceded an equaliser to Oldham in the seventh minute of stoppage time to remain third, a point further back.
Nick Blackman's 52nd-minute penalty looked set to decide the game, but Matt Smith stunned Bramall Lane by making it 1-1.
Crawley looked to have squandered a 2-0 lead against basement boys Bury only for a Nicky Adams winner in the fourth minute of injury time to give them a 3-2 win which sent them fourth.
Goals from Adams and Hope Akpan either side of half-time put Crawley in command, but Tom Hopper and Andy Bishop scored in the space of four minutes as Bury showed plenty of fighting spirit to level.
Adams got his second at the death, though, to leave Crawley a point off second.
Notts County claimed a thumping 4-0 away win at sorry Carlisle to go fifth.
Jeff Hughes (11), Neal Bishop (27), Francois Zoko (54) and a Jamal Campbell-Ryce penalty (57) put the Cumbrians to the sword.
The win left County level on points with sixth-placed Swindon, who staged a late comeback to rescue a 2-2 draw at home to Coventry.
A first-half brace from David McGoldrick put City in control, but Gary Roberts halved the deficit in the 77th minute and James Collins earned Town a point three minutes later.
Eddie Howe's second stint in charge of Bournemouth got off to a winning start with a 2-0 victory at home to Leyton Orient which lifted the south coast club out of the relegation zone.
Lewis Grabban (65) and Marc Pugh (67) scored to give the former Burnley boss an ideal start.
Brentford were made to pay for a missed penalty as they drew 1-1 at 10-man Scunthorpe.
Clayton Donaldson missed from the spot in the 34th minute, but Harry Forrester did put the Bees ahead two minutes before the break.
But Leon Clarke levelled in the 77th minute and the Iron held on following David Mirfin's late red card.
Doncaster scored an 89th-minute equaliser through Rob Jones to snatch a 1-1 draw at struggling Hartlepool.
Neil Austin put the hosts ahead from the spot in the 70th minute.
Portsmouth saw off Crewe 2-0 thanks to a second-minute Wes Thomas effort and an Izale McLeod penalty in the 18th minute.
