Kicking with the wind, the Magpies held the Giants scoreless and kicked two goals in the last term for their 4.9 (33) to 4.1 (25) win.
The Giants suffered what looked to be a major blow in the final term on Saturday at Victoria Park when captain Bec Beeson seemingly hurt her left knee and had to leave the ground.
But she was able to return, with GWS later explaining it was cramp.
It is the first win for the Collingwood women since September 27, on the way to the wooden spoon last season with a 1-10 record.
The Magpies hit the lead for the first time since the opening term when veteran Sabrina Frederick marked a risky defensive kick and goalled.
A few minutes later, the Giants were deep in attack and looked like they could regain the lead, when hard-nut Irish defender Muireann Atkinson laid an outstanding tackle on Taylah Levy.
Collingwood then moved the ball down the ground and Grace Campbell kicked the sealer.
Beeson had an absorbing duel in the midfield with Britt Bonnici, who was best afield with 22 disposals and seven clearances.
Tarni Evans kicked three goals in the first term for GWS, including a booming shot that will be a candidate for goal of the season.
But Lucy Cronin then shut down Evans, while Imogen Barnett impressed in the ruck for the Magpies.
It was a fierce contest with plenty of heavy clashes, particularly a second-term collision that forced Collingwood's Tarni White and Giants opponent Brodee Mowbray from the field. They were able to play out the match.
Magpie Kalinda Howarth, who kicked the first goal of the game, was in tears after Cambridge McCormick caught her in a brutal tackle.
Howarth left the field holding her right shoulder, but also returned to play out the game.
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