The tournament's top seed claimed his 34th career ATP singles title and his second straight crown at Qatar to become the first player to win back-to-back crowns in Doha since Stefan Edberg in 1994-95.
Federer rose to 34-9 lifetime in Qatar finals and collected $142,000.
He was 81-4 in 2005 and captured 11 titles, including Wimbledon and the U.S. Open. His 24-match winning streak was broken by David Nalbandian at the Tennis Masters Cup in November.
"I knew that all it takes is the chance of one big win for a young player to break through," said Federer. "So I knew that this was a dangerous match."
Monfils, 19, the seventh seed in this event, dropped to 1-3 in finals.