A 3-6 6-1 6-1 victory in one hour and 44 minutes earned Bencic a fourth career WTA Tour title and a second of her resurgent 2019.
Bencic booked her place in the WTA Finals in Shenzhen with her semi-final victory over Kristina Mladenovic and capped the week with a Premier title.
It came after a shaky start in which she dropped the opening game on serve and was later broken again en route to losing the first set.
But she struck on Pavlyuchenkova's serve in the first game of the next set to immediately launch her comeback and broke on a further two occasions to level the match.
Bencic, the world number 10, was in control and raced 5-0 up in the decider, converting her first championship point soon after when Pavlyuchenkova smashed a return into the net.
After her poor opening set, the Swiss star did not allow 2014 champion Pavlyuchenkova a single break point in her dominant second and third sets.
"It feels unbelievable right now, I still can't imagine it," said Bencic, who was the third seed in Moscow.
"I had no pressure going into this match. We were so happy on Saturday celebrating Shenzhen and this is the cherry on top."