The Swans came into the match on top of the ladder and riding a nine-game winning streak, but they hadn't beaten the Pies since 2005, and that record has continued in Collingwood's 12.6 (78) to 9.16 (70) triumph.
Thomas appeared to hurt his knee after a heavy tackle from Shane Mumford in the opening minutes and, while he tried to keep playing, he was substituted early in the second quarter for Alan Didak.
The Pies will be sweating on the diagnosis of his knee injury, but they will get an enormous boost from becoming the first side to knock off the Swans since St Kilda in round nine.
In the absence of ball-magnet Dane Swan, Dayne Beams and Sharrod Wellingham picked up the slack, with Beams finishing the game with 34 possessions and three goals, including the sealer in the final 30 seconds. Wellingham had 24 possessions and an impressive 11 tackles.
Josh Kennedy (40 possessions, eight tackles) was absolutely monumental for the Swans in a losing cause, with Lewis Roberts-Thomson kicking two goals, but it is Collingwood now matching the Swans' 15-4 record for the season.
Ladder leaders for the past five weeks, the Swans' top-four hopes took a jolt, with games against Hawthorn and Geelong still to come.
The Swans dictated terms for the opening 10 minutes of the match, leading to a Roberts-Thomson goal, but the Pies lifted their work rate and soon assumed control.
Thomas, Travis Cloke and Paul Seedsman kicked goals in a five-minute spell midway through the term as Collingwood made its customary fast start against the Swans.
In their 10-game winning run against the Swans, the Pies won nine opening quarters, and once again they built an 11-point lead at the first change.
In a game of momentum swings, the home side was well on top to start the second term, suddenly finding some space where previously there had been none, leading to quick goals from Trent Dennis-Lane and Roberts-Thomson.
But the Pies weren't done, with the impressive Beams, and then the revitalised Didak, kicking majors to give their side a three-point edge at halftime.
The match was an intense arm-wrestle from that point, with the Swans building a 17-point lead midway through the third quarter which they weren't able to maintain.
Instead it was the Pies taking four points off the Swans one more time and significantly boosting their own top-four hopes.
SYDNEY SWANS 1.3 4.7 8.9 9.16 (70)
COLLINGWOOD 3.2 5.4 7.4 11.6 (78)
GOALS
Sydney Swans: Roberts-Thomson 2, Dennis-Lane, Bird, Goodes, Kennedy, O'Keefe, Pyke, McGlynn
Collingwood: Cloke 3, Beams 3, Blair, Didak, Seedsman, Wellingham, Fasolo, Thomas
BEST
Sydney Swans: Kennedy, O'Keefe, Richards, Roberts-Thomson, Parker, Jack
Collingwood: Beams, Wellingham, Seedsman, Maxwell, Cloke, Reid
INJURIES
Sydney Swans: Everitt (omitted) replaced in selected side by Armstrong
Collingwood: Thomas (knee), Clarke (thigh)
SUBSTITUTES
Sydney Swans: Trent Dennis-Lane replaced by Tony Armstrong in the final quarter
Collingwood: Alan Didak replaced Dale Thomas in the second quarter
Reports: Nil
Umpires: Rosebury, Nicholls, Jeffery
Official crowd: 45,827 at ANZ Stadium
The views in this article are those of the author and not necessarily those of the clubs or the AFL.
