Federer, who maintains a home in Dubai, delighted a packed stadium of fans who seemed biased for the Swiss in back-to-back wins over Novak Djokovic in the semifinals and Berdych.
"Things definitely went my way out here tonight," Federer said. "I've had a lot of tough matches in the last year and a half so it was nice to get a lucky break again."
The victory was hard fought as Federer lost the first serve and his serve in the second to trail 3-2.
Federer's win, his sixth here in the last 12 years, extends his record of winning at least one title a year to 14 consecutive years.
This is Federer's first tournament victory since winning in Halle, his only title of 2013, last June.
Federer improved his record over Berdych to 12-6 with the win. The last time they played, however, Berdych beat Federer in the Dubai semifinals last year.
"He's the greatest player of all time and he'll never give up and give you anything for free," Berdych said. "I knew that and thought I was ready for it, but my execution wasn't good enough to hold it to the end."
The loss ended Berdych's longest winning streak of his career at 11 matches.
In the first set, the fourth-seeded Federer's forehand looked shaky and he appeared a step slow.
After exchanging early service breaks, the third-seeded Berdych snared the go-ahead break in the sixth game. On a second break point at 30-40, Federer netted a backhand to lose serve.
In the second set, there was another early exchange of breaks. From 4-4, Federer won the final eight points of the set to even the set score.
"Everything happens very, very quickly and I was looking for better serving because that's what let me down the most in the beginning, getting broken three times in five, six service games," Federer said.
Both players had break opportunities in the first two games of the third set — Berdych three and Federer one — but each held.
Federer secured his way to victory when he broke Berdych on a second break point in the fourth game.
The Swiss faced two break points on his serve in the seventh game but held on for 5-2.
Berdych was able to save two Federer match points on his own serve in the eighth game. But the Czech couldn't stop Federer from serving out. On Federer's third match point at 40-15 in the ninth game, Berdych netted a backhand return.
"The match started pretty well and I had many chances," Berdych said. "It's very disappointing for me the way I handled that situation."