The Dockers struggled for fluency in last week's 36-point loss to Gold Coast in the wet, and a pre-match downpour on Sunday ensured another slippery affair.
The Magpies were dealt a blow midway through the second quarter when ruckman Mason Cox was subbed off with a finger injury.
But his replacement Henry became an unlikely hero, with the 19-year-old booting four second-half goals to help propel Collingwood to the 12.8 (80) to 6.8 (44) victory.
Will Hoskin-Elliott, Brody Mihocek and emerging star Jack Ginnivan shared the load up forward with two goals apiece, with Henry dominating after half-time.
Ginnivan earned the ire of Fremantle fans in the final term when he outmarked Brennan Cox and celebrated in front of the Dockers' faithful while he strolled in to kick the easiest of goals.
The win improved Collingwood's record to 5-5 ahead of next Sunday's MCG blockbuster against arch rivals Carlton.
Fremantle started the season with a stunning 7-1 record, but back-to-back losses in the wet have raised serious questions about whether their game plan can hold up in slippery conditions.
Big splashes of water were seen whenever a player hit the turf early in Sunday's match.
Collingwood forward Jamie Elliott almost took a mark-of-the-year contender in the first quarter, while Nathan Murphy was forced off briefly for treatment after being crunched by Andrew Brayshaw.
Jordan De Goey's class ensured scores were tied at quarter time, and the Magpies pulled clear in the second quarter on the back of three unanswered goals.
Hoskin Elliott's pack mark and goal early in the third term set alarm bells ringing for Fremantle, but a clever snap from Michael Walters in the opening minutes of the last quarter saw the Dockers close the margin back to 16 points.
Henry starred from that point on, booting three goals in the last term to kill off Fremantle's resistance.
Will Brodie (36 disposals, 11 clearances) and David Mundy (35 possessions) led the way for Fremantle.
Collingwood lost the possession count by 49 and contested possessions by 23.
But their efficiency with the ball meant they won the inside 50m count 60-46, allowing their forwards to kick a winning score.Â
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