Ivanovic's impressive form in Melbourne offered hope she could be reclaiming the kind of form which saw her land the 2008 French Open - the last time she advanced to the last eight at a major - and reach the top of the world rankings.
And although she held her own for much of the contest, especially towards the end of the second set as Kvitova's focus deserted her, the Wimbledon champion possessed too much power and guile for the Serbian.
"She is a tough opponent," said Ivanovic.
"You really have to try to get a swing on the ball and hope you get some rhythm and that's going to cause some errors. That's what happened to me today [Monday].
"But it has been a nice tournament for me, I played some really good tennis and proved to myself that I can play at that level and compete against the best."
Kvitova broke serve twice in the first set and seemed on course for a straightforward victory when she broke again for a 3-2 lead in the second.
But a freak incident in the ninth game, which saw the Czech take an airshot at a simple smash, seemed to throw her off course.
She was broken to love when serving for the match and also lost the following game to love as Ivanovic ramped up the pressure.
Kvitova regained her composure to take it to a tie-break in which Ivanovic's problems on serve resurfaced.
"It was a tough match, especially at the end," Kvitova said. "I lost eight points in a row but I was happy with how I played in the tie-break."
Kvitova will play Sara Errani in the quarter-finals, after the Italian comfortably beat China's Zheng Jie 6-2, 6-1 at the Margaret Court Arena.
Joining them in the last eight are Russian duo Maria Sharapova and Ekaterina Makarova.
Sharapova did well to recover from a set down to beat Sabine Lisicki 3-6 6-2 6-3, while Makarova claimed the scalp of Serena Williams with an impressive 6-2 6-3 victory.
Australian Open Day 8 Women's 4th Round Results
Petra Kvitova def. Ana Ivanovic 6-2 7-6
Sara Errani def. Jie Zheng 6-2 6-1