Having dominated the first half to lead by 44 points at the main break, the Dockers were headed by the Magpies when Caolan Mooney kicked his first goal four minutes into the last quarter.
But the home side rallied to kick the last five goals of the match to claim their fifth win of the season, 15.10 (100) to 10.13 (73).
Fremantle simply mauled the Magpies in the opening term.
The pressure of the Dockers was immense. They outnumbered the Magpies at every contest and their run and spread, led by David Mundy, was extraordinary.
Fremantle had 124 disposals in the opening term, the most of any team to quarter-time this season.
But a knee injury suffered by ruckman Jon Griffin might have been a turning point, albeit not immediately.
The 27-year-old has been one of the Dockers' key players this season in the absence of Aaron Sandilands.
But when he was subbed out in the opening term, after his right knee gave way during a ruck contest, Fremantle's dominance at the stoppages eased.
After Tendai Mzungu goaled eight minutes into the second term to extend Fremantle's lead past seven goals, Collingwood took control of the clearances and the momentum.
But their inaccuracy meant the Magpies still trailed by 36 at the major change.
However, the third term was all Collingwood and Dane Swan was the spark. The 2011 Brownlow medallist was moved forward with instant impact, kicking two brilliant goals and having a hand in two others.
The Magpies kicked six goals to one for the quarter, echoing the Dockers' round three loss to Essendon when they conceded five goals to none in the third term after leading by 36 points at half-time.
But Fremantle dug deep and steadied.
Jack Hannath, who stood tall in Griffin's absence, took a strong mark and kicked truly to reclaim the lead before the skill and smarts of Michael Walters finished the Magpies off.
He kicked two of his four goals in the last 12 minutes to ignite the crowd and consign the Magpies to their third defeat.
It is also the fourth time they have conceded 100 points or more this season.
FREMANTLE 6.4 9.6 10.7 15.10 (100)
COLLINGWOOD 1.2 3.6 9.8 10.13 (73)
GOALS
Fremantle: Walters 4, Mayne 2, Ballantyne, Mundy, de Boer, Sutcliffe, Mzungu, Pearce, Silvagni, Hannath, Crozier.
Collingwood: Swan 2, Krakouer 2, Dwyer 2, Sidebottom, Blair, Kennedy, Mooney.
BEST
Fremantle: Ibbotson, Duffield, McPharlin, Walters, Barlow, Mundy, Suban.
Collingwood: Swan, Reid, D Thomas, Sidebottom, Dwyer, J Thomas, Shaw.
INJURIES
Fremantle: Stephen Hill (quad) replaced in selected side by Cameron Sutcliffe, Griffin (knee).
Collingwood: Clarke (hamstring), Mooney (knee).
SUBSTITUTES
Fremantle: Hayden Crozier replaced Jonathon Griffin (knee) in the first quarter.
Collingwood: Caolan Mooney replaced Marty Clarke (hamstring) in the second term.
Reports: TBA
Umpires: Margetts, Mollison, McInerney
Official crowd: 37,214 at Patersons Stadium
