Federer, playing his first tournament in Japan turned in a dominating performance to see off the 10th seeded Henman and win his 42nd career title.
"I beat Tim at Wimbledon and the U.S. Open this year but I thought this might be the most dangerous one," said Federer after his sixth straight victory over Henman.
"It's over three sets and the surface is fast. It was fantastic. I had to come up with some great passing shots at the right time."
Henman's game imploded in the sixth game of the first set when the former British number one handed Federer his first break of the match after serving three consecutive double faults.
"I guess if you look at it very harshly that cost him the match," Federer said.
"It's like giving it away. If he wants to win that's just a thing he can't do.
"Those three double faults definitely gave me the first set. It gave me a cushion and put the pressure on Tim," the Swiss player added.
Henman, who won the last of his 11 career titles at the Paris Masters in 2003, was just happy to back in a final, having lost his last one also to Federer at Indian Wells in 2004.
"I'm not the first guy to lose to Roger and I won't be the last," said Henman.
"I tried to mix it up as much as possible but he was able to come up with phenomenal passing shots.
"It's definitely been a fantastic week for me with the level I've played. It's great motivation and to be back in a big final is fantastic."
Federer's win gave him a record of 42 wins in 55 finals appearances which is the best finals win-loss ratio in Open era history.