Victory in 77 minutes gave the 22-year-old his second trophy in 2013 after he won the now-defunct San Jose title for a third straight year in February.
Raonic won with 18 aces, including a final untouchable serve in which he set up two match points against his Czech opponent, the only player in the ATP top 10 still without a 2013 title.
The Canadian winner converted on his first opportunity with a down-the-line winner.
"Of course, it feels great to win the title," said Raonic, 37-17 on the season.
"The first set was about finding rhythm. Once I did I was solid after that.
"I knew I had to play slightly more aggressive, not just put the ball in play. I did that and was able to take control, I got some insight into what I needed to do to beat him.
"It was great to be back on hardcourt. I got some confidence and that is what I needed this week."
Raonic has won won five times in nine finals - all on the hardcourt which suits his big-hitting game. His victory over Berdych improved his record against top 10 opponents to 12-20 over his career.
His victory came after he defeated two seeds and top 10 players (Berdych and Richard Gasquet) in semi-final and final rounds on the way to a trophy (after Chennai in 2012).
Raonic was flying overnight to Tokyo to get set for his start at that event where he lost the 2012 final to Japan's Kei Nishikori.
The win was the second for Raonic against Berdych after beating the Czech in Cincinnati last season. Berdych won his last title in Stockholm last October.
"Milos played outstanding today and he deserved to win. But I still had a great week, I didn't get the title but I almost got there," said Berdych.
"I've been playing well and I can take this form to Beijing next week. For me, this was still a good week even if I missed the title."
Raonic, coached by 2006 Bangkok runner-up Ivan Ljubicic, will keep his head down as he continues on in the final stretch of the season.
"The team and I will just keep plugging away and working hard. A lot of things are going well right now," he said.