Coming off a bye, the Hawks were outplayed for much of the game, and twice trailed by 17 points during the early stages of the third quarter.
But they booted four goals to two in the final term, winning 15.12 (102) to 13.9 (87) for their 10th straight win this season.
Five talking points: Carlton v Hawthorn
It was Hawthorn’s 10th victory in a row over the Blues, who haven’t beaten the Hawks since round six, 2005.
The contest went down to the wire, with Blues sharp-shooter Eddie Betts missing a chance to bring his team within four points with just two minutes remaining.
A great pass from Hawthorn big man Jarryd Roughead then allowed speedster Bradley Hill to seal the result in the dying seconds.
Carlton was left to rue the loss of skipper Marc Murphy during the second quarter after he suffered a fractured cheekbone in a clash with Hawthorn captain Luke Hodge.
After the game, Hodge said the contact was not intentional.
"I went in for the ball and we clashed, and all I remember is going to follow up," he said.
"It was a ball-up and I turned around and he was on the ground. The first thing, I was like, 'Gee, I hope he's OK'.
Despite losing Murphy, who is the club's No. 1 midfielder according to the Official AFL Player Ratings, the Blues still won the possession count and won 52 clearances to 30.
"You lose your captain, against a side like this, of course it has an impact," Carlton coach Mick Malthouse said after the match.
"I don't think we lost because of that. It certainly didn't help."
Malthouse was left furious with the adjudication of the holding the ball rule on a night when the Blues lost the free kick count 22-13, including 14-4 Hawthorn’s way in the second half.
"We squared them off nearly everywhere – free kick count we didn't, metres (gained) were slightly skewiff, but everywhere else I thought we did pretty well," he said.
"Couldn't fault the effort."
But thanks to a number of inspirational acts from Hodge and eight goals between Roughead and Lance Franklin, the Hawks extended their perfect run since losing in round one to Geelong.
"It was really good for us," victorious coach Alastair Clarkson said after the match.
"You never, as a coach, like games to pan out the way that one did.
"But it's really pleasing we found a way to grind the game out and get ourselves in front on the scoreboard when we were well beaten at the clearances."
Sam Mitchell (24 possessions and a goal) and Grant Birchall (23 touches) were the leading ball-winners for Clarkson's side, while defender Josh Gibson held Carlton spearhead Jarrad Waite to only 11 possessions and two goals.
Hodge's numbers (15 possessions, four marks, one goal) might not look spectacular on paper, but he repeatedly dragged his team back into the contest with strong bumps, tackles and courageous marks.
However, his high contact on Blues defender Lachie Henderson during the second term is likely to attract the attention of the Match Review Panel.
Click here to vote for the three best Hawthorn players from the game
Carlton conceded the opening three goals of the game, but Mitch Robinson, who was unhappy to be subbed out during the narrow loss Essendon the previous week, was the catalyst behind its impressive comeback.
Robinson kicked a goal and laid some bone-crunching tackles as the Blues closed to within two points at the first change.
By the mid-point of the second term, Malthouse's men had booted six of the last seven goals, but the loss of Murphy and a shoulder injury suffered by Robinson just before half-time proved costly.
Click here to vote for the three best Carlton players from the game
In his 250th game, Chris Judd (29 possessions, nine clearances, one goal) was a standout performer in the midfield for Carlton, while Brock McLean (33 disposals, nine clearances) played his heart out.
Betts finished as Carlton's leading scorer with three majors.
The Blues have a bye next weekend, while Hawthorn will be aiming to post its 11th win of the season when it hosts West Coast at Etihad Stadium next Friday night.
Mitch Robinson battled on gamely despite suffering a second-quarter shoulder injury. Picture: AFL Media
CARLTON 4.2 8.5 11.6 13.9 (87)
HAWTHORN 4.4 6.6 11.8 15.12 (102)
GOALS
Carlton: Betts 3, Waite 2, Casboult, Robinson, Tuohy, Gibbs, Kreuzer, Judd, Rowe, Armfield
Hawthorn: Roughead 4, Franklin 4, Gunston 3, Hale, Mitchell, Hodge, Hill
BEST
Carlton: Gibbs, McLean, Judd, Simpson, Kreuzer, Waite, Robinson, Tuohy
Hawthorn: Mitchell, Roughead, Birchall, Hodge, Gunston, Franklin, Lake, Stratton
INJURIES
Carlton: Andrew Carrazzo (calf) replaced in selected side by Sam Rowe, Marc Murphy (fractured cheekbone)
Hawthorn: Nil
SUBSTITUTES
Carlton: Kane Lucas replaced Marc Murphy in the second quarter
Hawthorn: Jonathan Simpkin replaced Max Bailey in the third quarter
Reports: Nil
Umpires: Stevic, Nicholls, Chamberlain
Official crowd: 45,670 at Etihad Stadium
