Trailing until midway through the last quarter on Friday, the Bulldogs slotted eight goals to four in the second half to send Carlton 0-3 and add to the pressure rising at  Marvel Stadium.
Naughton put the Bulldogs back in front with 4.22 remaining, before James O'Donnell slotted the match-winner two minutes later to give his side a dramatic 12.11 (83) to 11.9 (75) victory.
After struggling for impact with five possessions, the left-footed Naughton snatched a mark from 30m out and calmly went back to snap it through for a goal to give his side the late lead.
"He was having a difficult night, and probably uncharacteristically we didn't kick it to his advantage," Bulldogs coach Luke Beveridge said.
"Just to hang in there for us and kick what was a pretty difficult goal, crucial in the outcome.
"He just had his moment and took it and all his teammates were buoyed by it."
The loss continued a concerning trend for Carlton, who have kicked a combined eight goals in second halves across their three games in 2025.
Carlton captain Patrick Cripps was well held for most of the night, and suffered a huge knock to the hip when he flew for a mark during the third quarter.
Star Blues ruck Tom De Koning was arguably best on ground, while emerging forward Brodie Kemp kicked a career-high five goals, including what could have been the match-winner.
Star forward Charlie Curnow responded after a poor game against Hawthorn, kicking three goals, but the task was left to too few for the Blues.
"I felt like we lacked composure for different times throughout the game," Carlton coach Michael Voss said.
"Our best has been pretty good, but we just seem to be straying from us more than we'd like and it's giving little pockets of windows for an opposition to walk through a little bit."
Mature-aged recruit Sam Davidson (31 disposals), in just his third AFL game, was superb along with stand-in captain Tom Liberatore, who rallied after being well held early.
Carlton subbed off Zac Williams in the second quarter for Jordan Boyd after the forward experienced achilles and calf soreness.
It will be a concern for the Blues, with Williams having ruptured his achilles in 2018 when he played for GWS.
Williams suffered an ACL injury in 2023, and has battled soft-tissue problems since arriving at Carlton ahead of the 2021 season.
In a positive sign for the Bulldogs, troubled young gun Jamarra Ugle-Hagan attended the match with his teammates, only a week after he skipped the club's 100th anniversary game to be at the pub instead.
Ugle-Hagan has been given a flexible training schedule until he can fully commit to the program again and remains sidelined indefinitely.
Carlton face arch-rivals Collingwood on Thursday night in another monster match, while the Bulldogs travel to Optus Stadium to play Fremantle next Sunday.
