The Serb beat Federer 3-6, 6-3, 7-6 (7-3) Sunday to add another title to those he captured in the California desert in 2008 and 2011.
"I think I played a good game to break back," Federer said. "Got the first serve returns back, and then played well from the baseline.
"He (Djokovic) took advantage of that," he said. "So it was an interesting end to the match, no doubt.
"I think he played well. At the end he made sure he kept the ball in play and I might have made a few too many errors when it really mattered," said Federer.
The Swiss had won the event four times: in 2004, 2005, 2006 and 2012.