The Serb made hard work of his 6-3 6-7(5) 6-2 victory in the BNP Paribas Open final, giving up the second set after serving three double-faults, but he recovered to clinch a fourth trophy at Indian Wells following victories in 2008, 2011 and 2014.
Djokovic joins Federer as the only other man to win the tournament four times.
Enjoying a fine season that started with a fifth Australian Open triumph, Djokovic thrashed semi-finalist Andy Murray, the man he beat at Melbourne Park, and showed the same ruthless efficiency in the opening set against Federer.
The Serb broke in the fifth game and with his powerful, deep returns caused constant problems for his opponent.
He dropped just four points on serve and after taking the opening set, it was hard to see how the 33-year-old Swiss could recover.
But Federer, trailing 4-3, lifted his game to break Djokovic, bringing the Californian crowd to their feet.
Djokovic served for the championship at 5-4 in the tiebreak but gave up two double-faults, allowing Federer to force a third set that had looked an unlikely prospect.
World number one Djokovic stole an early break and looked back in command at 2-0, but Federer rallied again to break back.
Ultimately it was double-faults from the Swiss that proved costly, allowing Djokovic to break again and then hold firm for victory.
"I thought overall it was a great match from my side, very solid, great intensity, great commitment to hit every ball," said Djokovic.
"Credit to Roger for fighting through. Showed again why he's a competitor and champion, somebody that never gives up. When we got to the third set obviously it was anybody's game."
Djokovic's win moved him above coach Boris Becker in terms of career ATP Tour wins and said the milestone had given him an extra push.
"It's a great milestone. I don't take anything for granted. I believe that I have to earn everything that I do.
"I always try to look for additional motivation, because that's something that is necessary, especially if you're playing on the highest level."
Federer paid tribute to his opponent's staying power.
"Novak did well to obviously sustain the lead for most of the match," he said. "I think he found an extra gear in the end. It was tough."
(Reporting by Simon Evans; editing by Gene Cherry and Ian Ransom)
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