The Serbian World No. 1 inflicted the Scot a 7-6 (7-3), 4-6, 6-0 defeat in the final in two and three-quarter hours, claiming his third title in a season that he started with a trophy at the Australian Open, Xinhua reported.
Djokovic becomes the first man to complete the Indian Wells-Miami US title double for a third time in his career. The Serb won the same hard-court events in 2011 and 2013.
"Winning the double again means a lot of positive things and contributes to my confidence," Djokovic said.
"I'm so tired now, and I really want to enjoy this win. I don't have much energy left. I've played a lot of matches. I need to rest for a week and then think about the clay season."
Djokovic took control of the third set and ran Murray ragged on the way to victory with 28 winners and breaks on five of 18 occasions.
Murray finished with 48 unforced errors but aced eight times.
Murray's loss will still move him up to third in the ATP rankings behind Djokovic and Roger Federer.
Since his September 2013 back surgery, Murray has lost his last 12 matches against top-three opponents. He last beat Djokovic in the 2013 Wimbledon final.