Jackson (hamstring), Nathan O'Driscoll (ankle) and Corey Wagner (calf) all suffered game-ending injuries in the third quarter of Sunday's 15.7 (97) to 12.9 (81) win at Optus Stadium.
The loss of Jackson (30 hit-outs) was a particularly big blow, given he was winning the ruck battle against Tim English.
The Bulldogs trailed by 32 points at halftime, but clawed the margin back to 10 points on the back of Sam Darcy's five-goal haul before Dockers youngster Murphy Reid kicked the sealer to the delight of the 41,491-strong crowd.
Darcy was huge for the Bulldogs with 5.0 and 11 marks from 21 disposals, while English (40 hit-outs) dominated after Jackson went out of the game.
Ex-Docker Rory Lobb, who dyed a red lobster on his head for his return to his former stomping ground, was booed every time he touched the ball, but held up well in defence.
Caleb Serong (38 disposals, 15 clearances) dominated in the midfield for Fremantle, while Josh Treacy and Michael Frederick kicked three goals apiece.
The result improved Fremantle's record to 2-2 ahead of next Sunday's Gather Round clash with struggling Richmond, while the Bulldogs (2-2) face defending premiers Brisbane at Norwood Oval on Saturday.
The Bulldogs dominated the inside-50 count 19-8 and overall possessions 117-68 in the opening term, with Darcy setting the tone with two goals, three contested marks and 10 disposals.
But remarkably it was Fremantle who led by two points at the first change, highlighted by two goals to Frederick and a shake-and-bake goal from Shai Bolton, who burned off Bailey Williams before kicking truly.
Darcy kicked his third goal early in the second term and the Bulldogs led by five points with seven minutes remaining in the half, before Fremantle turned the match on its head.
The Dockers kicked six straight goals in a scintillating finish to the term to take a 32-point lead into halftime.
Frederick started the rampage with a clever snapped set shot from near the boundary.
Second-gamer Isaiah Dudley followed it up with a nice crumbing goal, before Treacy kicked one from point-blank range.
Bailey Banfield read a ruck tap perfectly to snag the next one, before 150-game milestone man Andrew Brayshaw nailed one of his own with just 29 seconds remaining in the half to send the crowd wild.
It was pandemonium when Jeremy Sharp added another just six seconds before the siren, with the onslaught leaving Bulldogs players shell-shocked.
The Bulldogs made it a scrappier affair in the third quarter, and Fremantle fans vented their frustrations as the free kick count ballooned to 18-9 in favour of the visitors.
Fremantle headed to the final change with a 24-point lead, but with just two fit players left on the bench and the rest of the squad tiring, they had to dig deep to seal the win.
The Bulldogs subbed out Laitham Vandermeer (knee soreness) in the second quarter.
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