Having gone into the game as outsiders, the Dockers were 20 points down early in the second quarter, before they hauled themselves back into the contest with a five-goal run that handed them a four-point lead at the long break.
Ross Lyon's men then survived a torrid second half and won 12.15 (87) to 9.18 (72).
The game – the first final held in Geelong since 1897 – was littered with spot-fires.
There was no opening bounce after Cats forward James Podsiadly was handed a free kick for high contact from Fremantle defender Zac Dawson.
And the niggle continued even after the final siren, with Ryan Crowley exchanging words with Joel Selwood and midfielder Steve Johnson as the players were shaking hands.
It was only Fremantle's second win at Simonds Stadium in the club's history, and the Dockers became just the second team to defeat Geelong at the venue since round 21, 2007.
Midfielders Michael Barlow (32 disposals and three goals) and Nathan Fyfe (25 disposals, seven clearances) and defender Lee Spurr (28 touches, 10 marks) were among the heroes for Freo, who have earned themselves a week's rest and a berth in a preliminary final at home at Patersons Stadium.
Crowley was among a number of other Dockers players who played a crucial role in the result. He started on Geelong midfielder Mathew Stokes but gave his team a big boost by limiting the impact of Johnson after the Cats maestro had gathered 12 possessions in the first quarter.
Barlow was Fremantle's leading goal-scorer, while Matthew Pavlich proved dangerous at times but finished with 2.3 when he could easily have booted four or five goals.
However, Freo might be without Dawson for its preliminary final after he was reported for striking Podsiadly and also jumped in the air to bump Selwood in the head during the final quarter.
It was a case of history repeating for the Cats, who were also bundled out of last year's finals series by the Dockers.
Having lined up without key forward Tom Hawkins, who was a late withdrawal after suffering a recurrence of his back soreness, their forward line struggled so badly that Geelong finished with less than 10 goals for the first time since 2008.
Andrew Mackie gave the Cats his usual great service from half-back, while fellow triple premiership players Jimmy Bartel and Joel Corey were solid performers.
Defender Cameron Guthrie, who was one of the late inclusions when Hawkins and Taylor Hunt (ankle) were ruled out, also played one of the best games of his career.
Paul Chapman started his 250th game as the substitute, and he put his stamp on the match when he entered the fray, but he and his teammates won't want to remember this afternoon.
GEELONG 4.6 6.11 9.13 9.18 (72)
FREMANTLE 2.5 7.9 10.12 12.15 (87)
GOALS
Geelong: Podsiadly 3, Johnson 2, Corey, Vardy, Motlop, Duncan
Fremantle: Barlow 3, Pavlich 2, Hill 2, Walters, Ballantyne, Spurr, Sandilands, Mayne
BEST
Geelong: Mackie, Bartel, Corey, Guthrie, Taylor,
Fremantle: Barlow, Fyfe, Spurr, Mundy, Pearce
INJURIES
Geelong: Hawkins (back) replaced in selected side by Walker, Hunt (ankle) replaced in selected side by Guthrie. Enright (knee)
Fremantle: Silvagni (soreness) replaced in selected side by McPharlin, Suban (ankle)
SUBSTITUTES
Geelong: Paul Chapman replaced Corey Enright at half-time
Fremantle: Tom Sheridan replaced Nick Suban in the third quarter
Reports: Nil
Umpires: Stevic, Pannell, McInerney
Official crowd: TBC at Simonds Stadium
