She seized the advantage when she gained the only break of the tightly contested opening set on her first set point.
"I'm really overwhelmed and don't think I realized that I just won my fourth Monterrey trophy," Pavlyuchenkova, the second said.
"Some people just have four trophies in total, and I have four here! It's very special and it's a special place in my heart. It's where I won my first title -- and since won three more!"
Pavlyuchenkova seized the advantage when she gained the only break of the tightly contested opening set on her first set point.
"Playing the final against the number one player in the world is already very special, because everyone wants to compete against the number one," she said.
"You don't get so many chances to do it, so it was one opportunity for me today. Beating her feels amazing."
Kerber, who regained the world number one ranking in March with American Serena Williams sidelined by injury, was playing in her first final of 2017.
She dug in to win a tense third game of the second set, breaking for 4-2 and going on to level the match.
Pavlyuchenkova admitted she was feeling the strain in the second set, but she found an extra reserve of energy to tap as she raced to a 5-0 led in the third and served out for her ninth career title in just under two hours.
It was the second time Pavlyuchenkova has beaten Kerber in a Monterrey final. She downed the German in 2013 when she added a third crown to those she won in 2010 and 2011.