It was their 37th meeting and Federer's 6-3 7-5 victory means he leads the series 20-17.
Federer, 33, trails Nadal 23-10 with their last meeting more than a year ago at the Australian Open.
"I think it started as a semi-final rivalry, you know, because me and Rafa were ranked one and two and two and one for a long time, and he was always three or four," the 33-year-old told reporters.
"Then it changed. He became world number one and then we still played each other sometimes, like last year, in the semis, but we started to play each other more often in finals as well and in the bigger matches like the U.S. Open and Wimbledon now last year again and so forth.
"I think it's really become a very nice rivalry. I don't think we have to adjust our games very much. We can just play our game, and then the better man wins."
Djokovic got the better of Federer to win last year's Wimbledon title, but world number two Federer has begun the year in impressive fashion, bagging two titles.
He said he has grown to love playing in Dubai where he has now matched his record at Halle and Wimbledon.
"I had a rough first visit here to Dubai where I was accused of not putting in my best effort," he said.
"I came back the following year and won it and went on a roll. I really felt like I had something to prove after that, and I guess that's what got me to my winning ways here.
"The seventh title is quite unbelievable, sounds pretty crazy."
(Writing by Martyn Herman, editing by Ed Osmond)
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