Isner, the No. 2 seed, had to work hard for his victory, a marathon 6-7 (5-7), 7-6 (7-4), 6-3 decision over No. 3 seed Feliciano Lopez of Spain.
The American saved all eight of Lopez's break chances and fired 13 aces en route to the comeback win.
Isner's victory moved him to 7-0 on clay courts this year.
Fourth-seeded Monaco, meanwhile, got past American Michael Russell 5-7, 6-1, 6-4 in another long match, this one clocking in at nearly 2 1/2 hours.
The Argentine, who didn't face a break chance in the second set, will be seeking his fifth ATP title Sunday.