An injury-time equaliser from substitute Chris Greenacre snatched all three points away from the Swans at the Liberty Stadium.
The Swans looked to be heading for a crucial win after a first-half screamer from Alan Tate gave them the advantage.
But Greenacre broke Swansea hearts as their lead at the top of League One was cut to six points with both promotion rivals Doncaster and Carlisle picking up victories on a night of mixed emotions.
Swansea City: de Vries, Rangel, Austin, Tate ©, Lawrence, Butler, Pratley, Britton, Bodde, Robinson, Scotland. Subs: MacDonald, Bauza, Way, Brandy, Burgin.
Tranmere Rovers: Coyne, Stockdale, McLaren ©, Sherriff, Kay, Mullin, Moore, Ahmed, Chorley, Taylor, Myrie-Williams. Subs: Achterberg, Zola, Greenacre, Jones, Curran.
Ref: J Singh
Asst-refs: B J Malone, L Swabey
4th official: R G Vaughan
Att: 11,039 Away: 90
The Swans welcomed back Dennis Lawrence to the heart of the defence after a one-month and seven-game absence with a knee injury.
Big Den was the only change to the side that slipped up 2-1 against Millwall at the Liberty on Friday night. He replaced Kristian O'Leary.
With defenders Garry Monk (back) and Marcus Painter (hamstring) still out, 18-year-old left-back James Burgin kept his place on the bench.
Tranmere were without Ian Goodison (knee) and Steve Jennings (suspended), while Steve Davies and Chris Shuker (both knee) remained sidelined.
Antony Kay returned to the side after a bout of 'flu as Ronnie Moore looked to fire themselves back into the play-off places.
Match action
Swansea made a confident start as Jason Scotland had a goal-bound shot blocked within the first few minutes.
And it was a case of keeping possession for the first 10 minutes as the Swans enjoyed all the ball.
A patient build saw the home side create their first real chance after 13 minutes when Tom Butler and Angel Rangel combined well down the right. The ball dropped kindly for Scotland who on his weaker foot brought a good save out of Danny Coyne.
Three minutes later and Scotland found himself with another good chance after picking up a loose pass from Andy Robinson. But again Coyne saved well with his legs.
Andrew Taylor was the first to get booked soon after for Tranmere after a foul on Butler, while Lawrence followed him for a foul on the edge of the area. Paul McLaren struck it, but Dorus de Vries pulled off a good save to push his effort around the post.
Play immediately swung to the other end where Scotland set up a shooting chance for Butler, but Coyne was down well to save with 22 minutes gone.
Some great skills from Robinson wide on the left nearly carved out the opening Swansea were desperate for. But Coyne managed to gather as Scotland closed in.
At the other end, Swansea were kept on their toes when a 25-yard shot from Jennison Myrie-Williams was well saved by de Vries in the 29th minute.
But the breakthrough eventually arrived two minutes before the interval when Scotland set up Bodde for a shot which was deflected for a corner.
Robinson took it, and when Ben Chorley's header dropped to Alan Tate just inside the area, the central defender smashed a fantastic volley beyond Coyne to bring the house down.
Half-time: Swans 1 Tranmere 0
Swansea made a sloppy start to the second-half as they gave the ball away too often. And they were given a timely warning that there was still plenty to do to secure the three points when Shane Sherriff did well to create a shooting chance which flew just wide.
It sparked a good spell for the visitors who were playing some good football themselves now.
But Swansea weathered the initial storm and slowly pulled themselves together as Scotland did well on the by-line before his shot was deflected behind for a corner at the near post.
Scotland was in again on the hour as a clearance from Tate caught out the Tranmere defence, but the striker delayed his shot long enough for Antony Kay to recover and clear the danger.
Tranmere created the next chance as they caught the Swans on a quick counter through Andrew Taylor, but de Vries saved well.
Tranmere created the next chance as they caught the Swans on a quick counter through Andrew Taylor, but de Vries saved well.
Swansea were starting to regain control again though as Robinson curled a 69th minute free-kick into the side netting, before Tranmere made the first substitution when Myrie-Williams was replaced by Chris Greenacre.
Swansea followed suit in the 73rd minute when Guillem Bauza replaced Scotland.
The home side knew they needed that second to kill the game off as Darren Pratley drove forward before firing a screamer just over the bar.
Taylor flashed a dangerous cross across the face of the Swansea goal with 14 minutes remaining as the home crowd held their breath, before Bauza forced a fine save from Coyne at the other end.
Roberto Martinez brought on fresh legs in the 82nd minute as Febian Brandy replaced the hard-working Robinson, before Bodde fired over after good approach play.
Brandy got into the action soon after as he drove in a cross which Bauza headed wide as Swansea looked to finish with a flourish.
Instead it was Tranmere who had the last word as McLaren broke down the right. The captain looked to be offside, but the flag never came and substitute Chris Greenacre fired home his cross a minute into injury time.
