The Lions, without their three best defenders and ruckman Mitch Clark, also lost Jared Brennan and Josh Drummond to serious injuries but managed to produced an amazing final-quarter fightback.
It was to no avail as the Dockers closed out their first-ever win in Brisbane in their ninth encounter dating back 15 years with a 15.23 (113) to 15.10 (100) triumph.
The match seemed over when the Dockers were 27 ahead at the 11-minute mark of the final term but the Lions' spirited scrapping effort reaped the next four goals.
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When Ash McGrath goaled from near the boundary line with seven minutes left, the home side was only six points behind.
It was Chris Mayne who finally sealed the win with two minutes left for Fremantle to continue their sensational 6-1 start to the season.
Without their two key defenders Daniel Merrett (hamstring) and Matt Magurie (suspended), as well as ruckman Mitch Clark (groin), the Lions were dealt a further blow before the start with defender Joel Patfull succumbing to a suspected hamstring strain.
They started like a house on fire to kick four of the first five goals before the visitors took control to take a 23-point lead into halftime.
When both Drummond and Brennan, two of Brisbane's best in the first half, were carried off in the third quarter the contest seemed over.
There were grave fears both injuries could be season ending as Drummond suffered a knee problem and Brennan, who landed awkwardly in a ruck contest, needed pain-killing gas for an ankle injury.
Fremantle skipper Matthew Pavlich's radar was off for much of the night but he still managed three goals to play a major role for the visitors as Brisbane's threadbare defence had little hope of stemming the flow.
Stephen Hill was superb for the visitors who added to their three-point quarter-time advantage with a 4.4 to 1.2 second quarter.
Mayne, Aaron Sandilands and Paul Hasleby were also stand-outs for the Dockers as they outplayed the home side in virtually all facets except for set shot kicking.
Dockers coach Mark Harvey rued their poor conversion rate but labelled it a significant victory for his young, rebuilding team.
Harvey heaped praise on his key defenders as Chris Tarrant ensured Jonathan Brown was ineffective and Luke McPharlin closely checked Brendan Fevola who did well to finish with three goals from limited opportunities.
Lions coach Michael Voss confirmed radar-boot Drummond was set to miss the rest of the year due to a ruptured anterior cruciate ligament that would require surgery.
The diagnosis was less clear for Brennan who will undergo scans but he could also be out for the season for his ankle injury
"The best case we could hope for is it's just bruised or torn ... but the suspicion is that it's a pretty major ankle injury on the way he's gone down," Voss said.
"Drummo looks like he's done his ACL so it's the worst news we could get."
