The 27-year-old world number one from Serbia also captured his fourth Indian Wells crown and is now tied with world number two Federer for the most men's titles in the California desert.
"The trophy is very heavy," Djokovic told the crowd as he celebrated adding to the titles he won in 2008 and 2011.
It was another epic struggle in a long list of hardcourt battles between the two top players in the world, who have met 38 times with Swiss great Federer still holding a slight 20-18 edge.
Djokovic also needed three sets to beat Federer in the 2014 Indian Wells title match.
Federer insisted people shouldn't read too much into this loss.
"I have beat him the last couple times. It is not like I lost 10 in a row," Federer said. "A lot depends on how well he serves and returns. We usually play in finals so we are both peaking at the same time."
The two have combined to win eight of the last 12 Indian Wells titles but this is the first time they have met in back-to-back finals.
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