Djokovic's win -- his sixth career victory in Miami to equal Andre Agassi's record -- saw him pocket $1.028 million (902,000 euros), taking him past Federer as the all-time ATP earnings leader with $98,199,548 to the Swiss great's $97,855,881.
"It was my best performance of the tournament," the 28-year-old Serbian said yesterday. "It came at the right time against a great player."
Djokovic's win also took him to a record 28th career ATP Masters title, one better than the old mark he shared with Spain's Rafael Nadal.
Sunday's victory was also Djokovic's 714th career win, moving him to 11th on the all-time list, one more than his coach, German six-time Grand Slam champion Boris Becker.
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"I'm grateful and proud of all the achievements," Djokovic said. "To put myself in position to have the records and be in the history books is a great accomplishment ... Hopefully I can make many more records."
- Novak's Miami springboard -
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Djokovic, who claimed his 63rd career ATP title, stretched his Miami win streak to 16 matches with his 30th victory in 31 starts over five years. His first Masters win came at Miami in 2007 and still inspires him.
Djokovic improved to 28-1 this year, the lone loss coming when an eye problem forced a Dubai quarter-final retirement against Spain's Feliciano Lopez.
Djokovic, who in January won at Doha and captured an 11th career Grand Slam title at the Australian Open, also swept the US double of Miami and Indian Wells for the third year in a row and fourth time overall.
"The most successful month of my career is March," Djokovic said. "I enjoy these two tournaments the most of any in my career."
- Nishikori feels pressure -
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Djokovic, who didn't drop a set at Miami, broke Nishikori in four of his first five service games to seize command.
"He played great tennis. That's why I couldn't play like I wanted," Nishikori said. "My serve wasn't going. It was a shame to have that because he had a great return and I felt a lot of pressure on my service games. He played good and I could have played a little better."
Nishikori surrendered a break to begin the second set with consecutive errant backhands.
Nishikori, who said his left knee was fine despite having a trainer treat it in the second set, hit a forehand long to be broken to end the match after 86 minutes.
"It's tough to find his weakness," Nishikori said. "He has great defense. It's tough to break his game."
As part of his victory celebration, Djokovic kissed his left hand and patted it on the court several times.
Nishikori, 26, was in only his second career ATP Masters final, after Madrid in 2014, while Djokovic was in his 11th consecutive such final, improving his record in that run to 56-2.