Berdych boosts London hopes with Beijing win
As a result of the win, he will move ahead of semi-final conquest Jo-Wilfried Tsonga in the ATP year-to-date rankings.
"I was really hanging in there. When I lost the first set, I knew I needed to start to play a little more aggressively or change something," said the world number 10.
Cilic, facing his first seeded player in this year's competition, set the tempo by breaking Berdych's serve in the second game.
Berdych's errors played a part in the first set which Cilic, who also lost the final two years ago, finished off with an ace.
"When I lost my serve and I was two breaks down, I was still positive," he said. "I think the key moment was a break at 5-4. Marin was serving and I made a set point and won the second set.
"From that moment I started to feel great; I had more energy for the third set."
Cilic admitted nerves had got the better of him as the Czech made his comeback.
"I had two advantages at 4-4 in the second set and maybe I [suffered] from a little bit of tension," he said. "He started to play better and I wasn't finding the right solutions."
Both players dripped sweat in the unseasonably humid Beijing autumn weather and the problems were compounded by a pall of smog enveloping the National Tennis Centre.
The air quality monitor at the United States Embassy in Beijing recorded "hazardous" levels throughout the final day of competition.