Former Wimbledon champion Kvitova was pushed hard at the Yale-staged tournament by her Russian opponent before taking a 7-6 (11/9) 7-5 victory.
The Czech took the Montreal title earlier in August and followed that by reaching the Cincinnati semi-finals.
She had lost to Kirilenko in the Olympic Games quarter-finals at Wimbledon so had plenty of incentive for their sixth career meeting, looking to lock up the series at three wins each.
Kvitova looked to have the opening set almost wrapped up when she moved 6-4 ahead in the tie-break, but Kirilenko was not finished and had her own chances to move in front.
It eventually went Kvitova's way, before the second set followed a pattern similar to the first, with neither player secure on serve. The first set had seen each player drop serve three times, and Kirilenko was an early break ahead in the second set.
But Kvitova turned it around, taking victory in two hours and eight minutes, and now her focus turns to the year's final grand slam, starting in New York on Monday. She starts as the fifth seed and plays Polona Hercog in the opening round.