A weary-looking Berdych saved one match point at 5-3 in the deciding set but Wawrinka sealed victory a game later with a swinging first serve that his opponent returned long.
"It's my first (ATP World Tour) 500 title and winning indoors is something special for me personally. It's always amazing to win a trophy. It's the best feeling," Wawrinka was quoted as saying on the ATP's website.
"It's been an amazing week. It wasn't easy, but every match I found my way. It was a great final. Tomas was playing really well, but I'm happy to turn that match for me and win the title."
It was Wawrinka's second title of the year after he triumphed in Chennai in January before falling at the semi-final stage of the Australian Open where he was defending champion.
Berdych felt he had let the match slip away from him.
"I'm disappointed with the way the match finished," he said. "I had my chances in the beginning of the second set and I didn't make them so I think that cost me the match."
(Writing by Martyn Herman, editing by Pritha Sarkar)
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