It was the first ATP title for Berdych since October 2012. Sunday's win allowed him to snap a three-match losing streak in ATP finals. He is 9-11 overall in championship matches.
Cilic, who won last week in Croatia, is 10-9 in finals.
Berdych fired off nine aces against no double faults in winning more than three-quarters of the points on serve against Cilic. He saved all three of the break points he faced, all of which came in the first set.
Cilic won a respectable 59 percent to the points when serving but Berdych cashed in one of his two first-set break chances and both of his opportunities in the second.
Berdych collected more than $450,000 along with the title, pushing his career winnings past the $17 million mark. Cilic's second-place check is worth about $204,000. He's won about $6.7 in his career.
Swim Week Miami Beach 2014 [PHOTOS]