The Russian's third career title Monterrey title was a 4-6, 6-2, 6-4 triumph over the German on the hard courts at Sierra Madre Tennis Club. Pavlyuchenkova overcame 13 double faults.
Pavlyuchenkova improved to 15-0 in her career at the event. She previously won back-to-back Monterrey titles in 2010 and 2011 before skipping the event last year to play in Dubai.
It was the fourth career WTA title for the 21-year-old.
Kerber, meanwhile, fell short in her bid for a first crown of the year.