It is the 20th title of his career and his second of the year after he won the Australian Open in January.
The second seeded Serbian is the only player apart from four-time champion Federer to have won the title three times, following Federer victories in 2003-5 and 2007.
He has now won 15 straight matches in Dubai and is enjoying a career-best 14-match winning streak dating back to December's Davis Cup final.
Federer looked the weaker player from the start and Djokovic surrendered just four points on serve in the opening set.
Djokovic was also aggressive from the baseline and he swiftly earned the first break of serve to lead 2-1 when Federer mis-hit a backhand wide.
Djokovic continued to pile on the pressure as Federer struggled to find a rhythm and he held two break points for a 4-1 lead. Although Federer held him off in that game, Djokovic broke again for the set when he forced Federer to net a backhand.
Federer broke to lead 2-1 in the second set, but his revival was short-lived.
A netted smash on break point allowed Djokovic to level at 3-3 and a backhand error from the Swiss gave him a further break for 5-3 as the Serb swept on toward his latest title.
