The meeting lasted 2 hours 37 minutes and ended with a score of 6: 7, 7: 6, 6: 2.
Kerber is the former first racket of the world and the winner of the Australian Open 2016.
In the quarterfinals, Pavlyuchenkova will play with Spaniard Garbigne Mugurusa, who defeated the representative of the Netherlands Kiki Bertens.
Earlier, Daniel Medvedev lost to Stan Wawrinka in the fourth round of the Australian Open.