Federer breezed through the first set before a battle in the second and came away with a 6-3, 7-6 (13-11) victory on Sunday, earning his third title of 2015. He previously won in Brisbane and Dubai.
The Swiss superstar also won a tournament in a 19th different country.
Federer took the first set in a mere 33 minutes thanks to a break of serve. He then broke for a 4-3 lead in the second, but Cuevas returned the favor in the very next game.
The 17-time Grand Slam champion nearly made three straight breaks, but couldn't take advantage of triple-break point in the ninth game as the native of Uruguay battled back to hold.
A grueling tiebreak then ensued and Federer saved a trio of set points before finally winning on his fifth match point.
Cuevas fell to 3-1 lifetime in finals, including 1-1 this year. He won in Sao Paulo in February.