Wimbledon champion Kvitova had looked in ominous form in the early stages, but it soon became apparent Kirilenko's movement was impaired by an injury to her upper left leg.
After breaking three times and displaying her best tennis in the tournament to date, Kvitova romped to a 5-0 lead, at which point Kirilenko had to leave Rod Laver Arena for a medical timeout.
The Russian returned with heavy strapping on her leg and despite her best efforts to make it a contest, Kvitova clinched the opening set and the first game of the second before Kirilenko called it a day at 6-0 1-0 down.
Kvitova will meet the winner of the clash between Ana Ivanovic and Vania King in round four.
Maria Sharapova also advanced with a 6-1 6-2 defeat of German Angelique Kerber.
Kerber, a semi-finalist at the US Open last year, was expected to provide the fourth seed with her first serious test of the tournament, but it never really materialised.
The scoreline may have flattered Sharapova but the outcome was never in doubt.
Sharapova outlined her intention by breaking in the first game and when Kerber double-faulted to make it 4-1 the signs were ominous for the 30th seed.
Another break secured the first set and the momentum remained with the Russian when she established a 2-0 lead in the second.
Kerber finally displayed the all-action style which took her to the last four at Flushing Meadows, hitting back to win a marathon game which featured nine deuces and then holding off a break point to level it at 2-2.
It was the first time in the tournament Sharapova had lost two games in a set and it seemed to push her on to greater heights.
The three-time grand slam winner broke for a 3-2 advantage and then extended her lead to 5-2 as Kerber wilted.
Sharapova served it out to advance to a meeting with Sabine Lisicki.
"It was a really good first set and she stepped it up in the second," Sharapova said.
"She was in the semis at the US Open and she has been on this stage before so I knew she could produce some good tennis.
"The second set was certainly closer than the scoreline suggests."
China got a second representative in the round of 16 as Zheng Jie recorded a surprise 6-3 6-3 win over former Wimbledon finalist Marion Bartoli.
Vera Zvonareva, the number seven seed, was another surprise loser, going down 7-6 6-1 to Ekaterina Makarova. Ana Ivanovic continued her recent revival though - beating Vania King 6-3 6-4 to enter the last-16.
Sabine Lisciki came from a set down to beat former French and US Open champion Svetlana Kuznetsova while Italian Sara Errani beat Sorana Cirstea, Samantha's Stosur's conquerer, 6-7 6-0 6-2.
In the last women's match of the day, Serena Williams powered through to a 6-1 6-1 win over Greta Arn.
Australian Open Day 6 Women's Results
Maria Sharapova def Angelique Kerber 6-1 6-2
Serena Williams def Greta Arn 6-1 6-1
Petra Kvitova def Maria Kirilenko 6-0 1-0 (ret)
Sara Errani def Sorana Cirstea 6-7 6-0 6-2
Zheng Jei def Marion Bartoli 6-3 6-3
Ekaterina Makarova def Vera Zvonareva 7-6 6-1
Ana Ivanovic def Vania King 6-3 6-4
Sabine Lisicki def Svetlana Kuznetsova 2-6 6-4 6-2