Two goals in a minute from Swansea City and a third in injury time saw Tranmere knocked out of the Carling Cup despite leading for much of the contest.
Enoch Showunmi's first goal for the Club put Rovers 1-0 up in an entertaining game at Prenton Park and the home side defended strongly to limit the chances for their Championship opponents.
However, the South Wales side netted twice in quick succession midway through the second half and added a third late in the game to end Rovers' hopes of reaching the third round.
It was a scoreline that didn't reflect the game with Rovers clapped off the pitch by the home fans for a performance full of effort and endeavour.
There was just one change to the side that started against Bournemouth with Max Blanchard making his first start in place of Nick Wood alongside Ian Goodison, while John Welsh was named as captain for the first time.
Swansea showed their classy passing skills right from the kick off, keeping possession for the opening minute until Ian Goodison won the ball from Joe Allen. The Jamaican almost let the visitors in for a chance on goal with an underhit back pass soon after but Joe Collister was quickly off his line to clear the danger.
Rovers' first attack started with an interception from Liam Darville and the youngster advanced well into the Swansea half before laying the ball off for Ian Thomas-Moore whose deep cross had to be turned out of the path of Terry Gornell for a corner.
Joss Labadie miss hit an attempt at curling into the top right corner on 18 minutes after good work from Enoch Showunmi, with the ball going well wide of the target from a promising position.
Goodison dealt well with Swansea's counter attack after Aaron Cresswell gave possession away in the visitors' half on 19 minutes, and the next chance of the game gave Rovers the lead.
Good defensive work from Welsh saw the midfielder pass back to Collister whose long clearance then forced Swans keeper Dorus De Vries off his line to come and claim the ball. However, he was beaten to by the head of Showunmi who then managed to hook the ball into an empty net from a tight angle to the delight of the home support.
Another long spell of impressive Swansea possession saw the visitors dominate possession for several minutes but Rovers were quick to close down and Brendan Rodgers' side were unable to find a way behind the Tranmere back line.
Cresswell almost picked out Showunmi with a wonderful cross through the six yard area after intercepting the ball inside the Swansea half but the striker was just unable to get his outstretched leg on the end of it.
Goodison cleared two Swansea crosses that were bound for black shirts inside the Rovers area around the 35 minute mark while Showunmi sprinted and barged his way past three challenges on the stroke of half time before winning a corner as Tranmere took their lead into the break.
Collister pulled off a fine save to deny Allen in the second minute of the second half after the winger ran on to a wonderful through ball from Andrea Orlandi.
The Swans continued to press and a header from Shefki Kuqi went just past the far post from Orlandi's well placed cross on 52 minutes.
Allen took advantage of a slip from Paul McLaren to test Collister with a low drive from 20 yards on 54 minutes, while Gornell sent an overhead kick past the target three minutes later at the other end after Showunmi missed with a header.
The visitors made a double change with Scott Sinclair and Stephen Dobbie introduced but the changes didn't make any immediate impact with Rovers pressing forward and Cresswell shooting at De Vries from Thomas-Moore's lay off on 63 minutes.
A sliced clearance from Goodison almost let Swansea in but Blanchard raced out of the six yard box to clear before Allen could shoot while Sinclair struck a free kick from a dangerous position over Collister's bar.
However, the visitors equalised on 73 minutes. A long range shot from Orlandi went over Collister, hit the bar, rebounded against Cedric van der Gun and with Collister still on the ground the ball rolled into the net.
A minute later the Swans were ahead, with Sinclair beating two defenders before stroking the ball across Collister and in at the far post.
Sinclair got inside Darville on 77 minutes but Collister was quickly off his line to prevent a third goal for the Swans and keep the contest alive, but the visitors went close again through Dobbie seconds later.
Labadie's powerful free kick brought a save out of De Vries on 81 minutes, with Adam McGurk and Lucas Akins brought on soon after in place of McLaren and Gornell.
An excellent tackle from Darville denied Sinclair a second on 88 minutes after the substitute had been superbly picked out by Dobbie.
Welsh tried a spectacular long range effort in the final minute of added time but it went over the bar and Rovers were knocked out of the competition moments later when Kuqi raced clear to fire past Collister for Swansea' third.
Tranmere: Collister, Darville, Blanchard, Goodison, Cresswell, Labadie, McLaren (McGurk 82), Welsh, Thomas-Moore, Showunmi, Gornell (Akins 82). Substitutes not used: Miotto, Bakayogo, Wood, Cathalina, Fraughan.
Swansea: De Vries, Williams, Taylor (Tate 87), Orlandi, van der Gun, Lopez (Dobbie 57), Monk, Serran, Allen, Thomas (Sinclair 57), Kuqi. Substitutes not used: Cornell, Donnelly, Richards, Walsh.
Referee: Mark Haywood
Yellow cards: Serran (60)