On a night when Ollie Hollands was withdrawn before the match in the wake of his brother's hospitalisation earlier in the week, the Blues trailed by just four points midway through the third quarter as a boilover loomed.
But a six-goal run from Fremantle killed off the contest, with Bolton kicking two of those early in the final quarter to help seal the 16.7 (103) to 13.11 (89) win in front of 54,100 fans on Saturday night.
Bolton was at his scintillating finest with 33 disposals, four clearances, eight tackles, two goals, three goal assists and 641m gained to win the Arthur Leggett Medal as best afield.
Jackson also showcased his star qualities, with his two goals on the run both coming after he sprinted forward immediately after contesting the centre-square throw-up - a rare feat for a ruckman.
The 24-year-old finished with 31 hit-outs and 21 disposals to easily win his ruck battle against former teammate Liam Reidy (22 hit-outs, 15 disposals).
For Carlton, captain Patrick Cripps (31 disposals, 11 clearances) and Sam Walsh (32 disposals) led the way, while Brodie Kemp kicked four goals and Mitch McGovern chipped in with three.
Fremantle's sixth win on the trot improved their season record to 6-1, while Carlton's finals hopes appear shot after moving to 1-6.
Carlton had been in the headlines all week following Elijah Hollands' high-profile mental-health episode against Collingwood, with the 24-year-old admitted to hospital on Monday.
His younger brother Ollie was initially named to play Fremantle and flew with the squad to Perth on Friday, but the Blues decided it was in his best interests not to play.
Fremantle were left with a few early worries to some of their key talls.
Spearhead Pat Voss was withdrawn just before the bounce because of illness, and Josh Treacy was left writhing in pain midway through the first term after hyper extending his right elbow in a big collision.
Treacy was able to shake off that knock to play out the term, and although Fremantle won the first 11 clearances of the match, they led by just 11 points at half-time.
The most bizarre moment of the second quarter came when a snaking snap from Jye Amiss was awarded a goal, despite the ball appearing to have not made it past the goal line before zagging away.
Cooper Lord had the chance to put Carlton in front midway through the third quarter, but his bouncing snap went just the other side of the post.
Fremantle settled from that point, with two quick goals from late inclusion Jeremy Sharp and then two majors from Bolton early in the final quarter sealing the win as the lead ballooned out to 41 points.
"A good team flexed," Carlton coach Michael Voss said.
"They flexed for that whatever it was - five, six, seven minutes of the (last) quarter."
Carlton at least kicked five of the last six goals to reduce the damage.
"It was a sloppy finish, which was disappointing, and took the gloss off what was a good night all around," Fremantle coach Justin Longmuir said of the late fadeout.
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