The striker placed his spot-kick into the roof of the net having earlier scored with a bullet header.
Shola Ameobi had given the Magpies the lead but they slumped to their fifth straight defeat.
The game began in bizarre fashion with referee Chris Foy being knocked down by a clearance. He was later substituted for fourth official Anthony Taylor.
Newcastle took the lead when Luke De Jong teed up Ameobi who flashed his shot across Michel Vorm.
The Magpies should have doubled their lead but Gouffran placed his header straight at the keeper.
But after losing Papiss Cisse and De Jong to injury, Newcastle suffered a further blow when Bony’s bullet header beat Tim Krul following a corner.
Newcastle dominated the second half with Dan Gosling’s low drive parried by Vorm while Loic Remy shot well wide from six yards out.
Swansea had chances through Jonathan De Guzman’s long-range effort which was inches over while Bony was put though on goal but was tackled by Krul as he tried to round the keeper.
But Swansea took the spoils when substitute Marvin Emnes was fouled by Cheick Tiote and Bony converted the penalty for his 21st goal of the season.
The result sees Newcastle stay in ninth while the Swans move up to 13th.
1' – CHRIS FOY FLATTENED: The referee is flattened from Coloccinni's clearance which hit him straight in the face. He gingerly gets to his feet.
16’ – INJURY: Cisse goes down clutching his knee and limps off to get treatment. He is substituted for Debauchy.
17’ – SWANSEA CHANCE: Bony's snap-shot deflects off Williamson for a corner after a good cross from De Guzman.
18’ CHANCE: Williams flashes a header across goal which is deflected for another corner.
22’ GOAL! Ameobi gets on the end of De Jong’s lay off and brushes past his marker before firing his shot across Michel Vorm.
30’ SUBSTITUTION: Referee Foy is going off after getting smacked by the ball earlier on and Anthony Taylor replaces him.
34’ – BONY SHOT: Bony nicks the ball off Tiote and smashes an effort wide from outside the box, decent effort.
40’ – REMY RETURN: Loic Remy comes on for the injured De Jong for his return to the side from injury.
43’ – MAGPIES CHANCE: Gouffran's free header from six yards is straight at the keeper.
45’+1 –GOAL! Davies' delivery is headed in by Bony running in following a corner.
47’ - GOOD SAVE: From a throw in, Gosling's low shot is tipped around the post by Vorm for a corner.
56’ – REMY MISS: Gosling squares the ball to Remy, but his shot goes well wide from six yards. He should have hit the target from there.
60’ – ANITA SHOT: Anita flashes a shot wide from the edge of the box across Vorm.
78’ – CHANCE: De Guzman's rasping effort from 25 yards finds the roof of the net, great hit.
82’ – GOOD SAVE: Krul darts off his line to get the ball off Bony who was through on goal after Emnes' through ball.
90’+2: PENALTY! Emnes is fouled by Tiote and Bony slams in the spot-kick for the winning goal.
Shola Ameobi’s goal was his first in the league since December 2012.
Newcastle scored a first-half league goal at St James’ Park for the first time in 2014.
Wilfried Bony’s last four league goals have come away from home – his previous eight for the club came at home.
Swansea are four points from safety with three games remaining.
TALKING POINT: Will Alan Pardew be in charge of Newcastle next season? Five straight defeats for a Newcastle side which have been in freefall since January. Since selling Yohan Cabaye, the Magpies have looked toothless in attack. Loic Remy returned today and they are reliant on his goals to salvage something from a woeful second half of the season. Critics will point to Pardew's ban for seven matches for headbutting David Meyler as contributing to his side's poor form.
MAN OF THE MATCH
Wilfried Bony (Swansea City): His power and movement gave the Magpies’ defence a headache. He scored an impressive goal with a bullet header after ghosting past his marker before netting an impressive penalty in stoppage time. Without his 21 goals this season, Swansea would have been in a far worse position this season.
Newcastle United: Krul 6, Coloccini 6, Williamson 5, Dummett 6, Anita 5, Gosling 7, Tiote 6, Gouffran 6, De Jong 6, Cisse 5, Sh Ameobi 8. Subs: Elliot, Debuchy 7, Armstrong 5, Remy 6.
Swansea City: Vorm 7, Rangel 5, Amat 5, Williams 6, Davies 6, Britton 5, Shelvey 6, De Guzman 7, Routledge 6, Hernandez 5, Bony 8. Subs: Bartley 5, Emnes 7.
MATCH IN A TWEET
- Sports & Recreation
- Newcastle United
- Wilfried Bony
- Swansea City
- Shola Ameobi
- Michel Vorm
- Loic Remy
- Jonathan De Guzman
- Luke De Jong