Melzer was leading Molfils 6-3, 2-1 in the final when the Frenchman withdrew from the U.S. Open tuneup citing an abdominal injury.
It marked the fifth career crown for Melzer and his first in an outdoor hardcourt event. His last victory came at the 2012 Memphis indoor tournament.
The Austrian breezed through the first set and was leading the second when Monfils appeared to hurt himself while serving and retired after receiving treatment during the changeover after the third game.
Melzer improved to 5-8 all-time in finals, while Monfils fell to 4-15 lifetime in finals, including 0-2 this year.