Third-seeded Bencic broke Pavlyuchenkova in the Russian's first service game in both the second and third sets.
Bencic hit eight aces despite landing just 54% of her first serves.
She's the first Swiss woman to win the Kremlin Cup since Martina Hingis in 2000.
The win capped a productive week for Bencic after she secured the last spot at the WTA Finals on Saturday. By qualifying for the Moscow final, Bencic overtook Serena Williams in the points ranking for qualification for the finals in Shenzhen, China.
The 22-year-old Russian is 2-2 in career finals after condemning his French opponent to his second consecutive defeat in Kremlin Cup finals after losing to Karen Khachanov last year.
Mannarino has lost eight of the nine ATP finals he's played, the sole exception coming with a win over Jordan Thompson in Rosmalen in June.