Former striker Wilfried Bony came back to haunt the Swans as he scored twice to help Stoke to a 3-1 victory at the bet365 Stadium on Halloween.
The Ivorian struck his first goal for his loan club after just three minutes, with Bony tapping home from ex Swan Joe Allen's goalbound effort.
The Swans were quick to respond as Wayne Routledge nodded home his first of the season in the eighth minute from Gylfi Sigurdsson's pinpoint cross.
The Swans did ride their luck, though, as Charlie Adam struck the post twice while Marko Arnautovic rounded Lukasz Fabianski only to see his shot hit the woodwork.
After the break, Stoke took the initiative with sub Ramadan Sobhi's shot being turned into his own net by Alfie Mawson.
The Potters wrapped up victory when Allen and Bony linked up once again. Allen's initial shot was saved, and when he squared to Bony, the striker headed home from two yards.
The Swans kept going, and Bob Bradley's side thought they had been awarded a penalty when Routledge was fouled by Erik Pieters. Referee Michael Oliver pointed to the spot, only to then award a free-kick following consultation with his assistant.
Defeat leaves the Swans on five points from ten games, with the next game seeing Manchester United visit the Liberty on Sunday.
The Swans made three changes to the starting XI in their 200th Premier League game.
Boss Bob Bradley, who named Gylfi Sigurdsson as captain, opted for Neil Taylor at left-back in a defence which saw Alfie Mawson retain his place after impressing in the home draw with Watford last time out.
Top scorer Leroy Fer returned to midfield in place of Leon Britton while the final change came up front with Fernando Llorente preferred to lead the line with record signing Borja among the subsitutes.
Also included on the bench was 18-year-old winger Daniel James, with the teenager - an unused subsitute in last season's FA Cup tie at Oxford United - promoted from the club's Under-23s side.
Ki Sung-Yueng, meanwhile, made his 100th league appearance for the Swans. It was also his 100th start in the Premier League.
STOKE: Lee Grant, Phil Bardsley, Erik Pieters, Joe Allen, Glenn Whelan, Marko Arnautovic (Peter Crouch, 86), Wilfried Bony (Jonathan Walters, 79), Bruno Martins Indi, Charlie Adam, Ryan Shawcross (capt), Xherdan Shaqiri (Ramadan Sobhi, 26).
SUBS: Shay Given, Marc Muniesa, Giannelli Imbula, Bojan.
SWANS: Lukasz Fabianski, Kyle Naughton (Angel Rangel, 41), Alfie Mawson, Mike van der Hoorn, Neil Taylor, Ki Sung-Yueng (Jack Cork, 86), Leroy Fer, Gylfi Sigurdsson (capt), Wayne Routledge, Modou Barrow (Borja, 62), Fernando Llorente.
SUBS: Kristoffer Nordfeldt, Jordi Amat, Leon Britton, Daniel James.
The Swans got off to a terrible start, with their two former players linking up to put them ahead after three minutes.
When Xherdan Shaqiri's corner was only headed high into the area by Neil Taylor, the ball was volleyed goalwards by Joe Allen and Wilfried Bony tapped home his first Stoke goal from close range.
Stoke's tails were up and they went close to doubling the lead when another corner found Ryan Shawcross, but his header was kept out by the diving Lukasz Fabianski.
The Swans needed a response, and they got one after eight minutes.
Fernando Llorente did well to control a throw in while holding off Bruno Martins Indi, and when the Spaniard touched to Gylfi Sigurdsson, the skipper found Wayne Routledge in the box and the winger rose above Phil Bardsley to nod home.
The hectic start continued with Bony's deflected shot dropping wide for a corner before Erik Pieters' powerful long drive fizzed past the far post.
It was entertaining stuff, and a third goal of the game was only denied by the woodwork. Marko Arnautovic teed up Charlie Adam, and the Scot's thunderous strike cannoned back off the post.
The Swans managed to carve open a couple of their own chances, with Sigurdsson's shot from inside the area deflected wide for a corner while the skipper later saw his left-footed effort comfortably kept put by Lee Grant.
But Stoke were back on it soon enough, and again the woodwork came to the Swans' rescue. Once again it was Adam, with the midfielder cutting back onto his left foot before unleashing a thunderbolt which clipped the far post.
Bob Bradley's side were riding their luck, and Stoke were wondering where their luck had gone after 39 muntes. After Allen slipped in Arnautovic, the Austrian rounded Fabianski but saw his shot deflect out.
The Swans needed a reply to ease the pressure, and Routledge drew a decent save from Grant after firing a half volley goalwards.
The visitors were forced into a change shortly before the break as Angel Rangel replaced Kyle Naughton, who picked up an injury.
But that was the end of an action-packed first half, which saw the Swans thankful for three efforts which were kept out by the woodwork.
HALF-TIME: Stoke 1 Swans 1
While the Swans endured some good fortune in the first half, after the break their luck run out.
It took Stoke ten minutes to regain the lead. Sub Ramadan Sobhi twisted and turned inside the box before his shot was knocked into his own net by the unfortunate Mawson.
The Swans were struggling to find space and use the ball to inflict damage on the hosts, and Bradley opted for another change as Borja came on for Barrow.
A big chance to equalise was wasted when Routledge latched onto Rangel's through ball, but the winger's decision to pass to Borja instead of going for goal was the wrong choice as the Stoke defence snuffed out the danger.
The game stretched further away from the Swans after 73 minutes as Bony grabbed his second and Stoke's third.
It came after Arnautovic's neat slipped pass sent Allen in on goal, and when his initial shot came back to him, he squared to Bony and the Ivorian nodded in from point-blank range.
The Swans looked for an instant reply as Llorente fed Borja, but his shot was deflected onto the crossbar and over for a corner.
The Swans then appeared to have been awarded a penalty after Routledge was fouled by Pieters. Referee Michael Oliver pointed to the spot, only to then switch his decision to a free-kick after consulting with his assistant.
That proved the end of a miserable night in Staffordshire for the Swans, who sit five points adrift of safety after ten games.