The Blues registered the first four goals of the match and still led by eight points at the final change before Fremantle kicked seven goals to one in a blistering last quarter to seal the 15.4 (94) to 10.7 (67) win in front of 39,358 fans.
Isaiah Dudley and Patrick Voss kicked two goals each in the final quarter onslaught, with the win improving Fremantle's record to 14-6 and keeping them just percentage adrift of fourth-placed Geelong.
Young injured his left groin late in the first quarter and was subbed out after being assessed on the bench.
The 24-year-old Young was playing just his third match back from hamstring surgery, and his latest setback is a massive blow with the finals little more than a month away.
"Touch wood, it's not too bad. It doesn't look very serious. He just couldn't get going," Longmuir said.
"I think today's injury was just a bit unlucky and a bit more of a twisting action."
Carlton were also dealt injury blows.
Blues youngster Harry O'Farrell, just minutes after kicking his first AFL goal in the second quarter, suffered a suspected ACL tear in his left knee after landing awkwardly in a marking contest.
"Shattering news for us and in particular him," Carlton coach Michael Voss said of O'Farrell, the No.40 pick from last year's national draft.
"The highs and lows of football - it's got a great way of being able to lift you up, and it's got a very nasty way of being able to bring you down as well.
"We've been so impressed with the young man, and he's going to evolve in a very good play for us."
Defender Adam Saad was left groggy and with blood pouring from his nose in the dying minutes after an accidental shin to the face from Andrew Brayshaw.
Fremantle's trio of spearheads Voss, Josh Treacy and Jye Amiss kicked three goals apiece in a potent attack, while Luke Jackson tallied 27 disposals, eight clearances, one goal and 18 hitouts in a huge display.
Dockers defender Jordan Clark racked up 30 possessions and 759m gained, and star midfielder Caleb Serong (19 disposals, eight clearances) fought back from a quiet first half under a tight tag from Cooper Lord.
George Hewett starred for Carlton with 36 disposals and seven clearances but was quelled somewhat after half-time by Jaeger O'Meara, while Patrick Cripps (36 disposals, nine clearances) tried his best to will the Blues over the line.
The scoreboard read 24-0 to Carlton before the most unlikely goal-kicker on the field - Fremantle defender Oscar McDonald - put the Dockers on the board after Tom De Koning coughed up a 50m penalty.
Carlton's early onslaught came courtesy of their clearance dominance and intense tackling pressure.
The Blues won the centre clearances 11-1 in the first half, helping them to a 24-point lead.
Hewett had 25 disposals and seven clearances to his name by the long break.
In contrast, Serong had just five possessions and two clearances.
Fremantle made their move in the third quarter with four goals to one - including two to Amiss - to close the margin to eight points at the final change.
Treacy was huge in the fightback, with his attack on the ball and powerful marking crucial.
The bustling spearhead nailed a set shot from 50m to put Fremantle ahead early in the final term, and the onslaught continued from there.
