The third-ranked Djokovic finished off Ferrer with an ace that was originally called out but was challenged by the Serb.
"That was an unusual way to finish the match, and something like this has never happened to me before," Djokovic said. "But what worked for me during the match was that I mixed the pace well, which I think, David does not like at all."
Djokovic was playing in his first final this year. He won the Australian Open in 2008, and added the Masters Cup title at the end of last season. At this year's Australian Open, he retired against Andy Roddick in the quarterfinals.
The top-seeded Djokovic broke Ferrer in the sixth game of the first set, but the fourth-seeded Spaniard broke back to 4-3. The players traded breaks again, but Djokovic got the decisive break in the final game of the set.
"This was a tough match because David is a very tough opponent," Djokovic said. "He is one of the hardest working players on the tour, and he just keeps running down every ball. He makes you earn every point."
In the second set, Djokovic led 2-0 before Ferrer recovered with a break in the seventh game. But Djokovic immediately broke back to lead 5-3, and then saved a break point before winning on the challenged ace.
"Nobody is a favorite in a final," Djokovic said. "Everyone has the motivation to do well. But I was physically and emotionally really involved with this tournament and to win it is a great feeling, because Dubai has a history of having one of the strongest fields on the tour. And despite some players pulling out, it was still a tough field."
Ferrer was also playing in his first final of the season.
"I played a very good game and I am very happy with what I did, but he was the better player in the end," Ferrer said. "However, I really enjoyed my week and am looking forward to more such consistent weeks in the future."