The Russian administered the first blow when she broke serve, but Pennetta immediately broke back before surging into a 5-3 lead.
After successfully serving for the first set, it was a tight battle in the second with neither player able to create a break point until the eighth game.
Pennetta saved two break points at 4-4, but she was broken two games later as Pavlyuchenkova kept herself in contention for victory by taking the second set.
It was an ideal start to the decider for the Russian as she broke serve at the first time of asking and after getting broken at 3-2, she managed to break back and hold to give her a crucial 5-2 lead.
Pavlyuchenkova had to hold off some pressure from her opponent, but she was able to see it through and claim a place in the quarter-finals.