The latest triumph puts the 36-year-old equal second with Ivan Lendl on the list of the most successful male players since tennis became a professional sport in 1968. Jimmy Connors leads the way with 109 titles.
Federer's Sunday triumph is his sixth title of 2017. Nadal too has six crowns this year including the French Open.
In January, after six months out to nurse an injured knee and back, Federer made a spectacular return winning the Australian Open in Melbourne - beating Nadal over five sets in the final - to seize his 18th Grand Slam trophy.
He overcame Nadal in the last 16 on his way to the Indian Wells Masters in March and beat the Spaniard in the final at the Miami Masters in April. Federer claimed Halle and Wimbledon during the grass court season.
But it was Nadal who went into Sunday's showdown as favourite having claimed the US Open in September and the Beijing Open on 8 October.
But on centre court at the Qi Zhong Tennis Centre, Federer started more dynamically taking Nadal's opening service game and then holding his own service to lead 2-0. He went on to take the opener in 37 minutes.
The expected response from Nadal failed to materialise. Federer broke to lead 3-1 in the second set and cruised home to win in 71 minutes.
"We didn't think maybe we were going to have the year we're having," said Federer. "I definitely didn't. Hopefully there's more to come."
"I played a fantastic tournament, having very good wins," said Nadal. "I am very pleased the way I played the whole Asian tour for me. Beijing and Shanghai have been a very positive two weeks for me. A lot of points, a lot of victories against great opponents. I come back with very good personal satisfaction the way that I played."
The world number one added: "It was a very difficult match for me. Roger played very fast and he played well. I could have done some things better, but that's it. He just played too good. That's my point of view. So congrats to him."