Djokovic collapsed on his back before tearing off his shirt after triumphing 5-7 7-6 (9-7) 7-6 (7-4) in Sunday's nearly four hour contest to get revenge after his loss to the Spaniard in last month's Wimbledon final.
The 23-time grand slam champion looked hobbled by the intense humidity at the tail end of the first set, barely moving when Alcaraz hit a backhand winner to grab the opener.
Alcaraz, who looked fresh despite being on court for more than 10 hours this week including wins over Australians Jordan Thompson and Max Purcell, grabbed a 4-2 second-set lead and it appeared he might cruise to the finish line.
But the 20-year-old Spanish sensation would produce a terrible service game while leading 4-3 that included four unforced errors and threw a lifeline to the world No.2.
In the second-set tiebreak Djokovic saved a championship point and went on to force a decider after winning a 25-shot rally.
During the break before the third set, a frustrated Alcaraz pounded his hand against the plastic drinks container next to his chair, requiring a medical time out to tape his finger.
In the decider, Djokovic broke on his fifth opportunity of the game for a 4-3 lead.
The drama would continue, with the Serb squandering two match points on return while leading 5-3.
Alcaraz would save two more match points and break serve when Djokovic missed an overhead for 5-5.
The players ultimately arrived at another tiebreak, which Djokovic won when his rival's forehand return went wide.
The win was Djokovic's 95th career title and 39th Masters 1000 crown.
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