It completed another bad day for organisers who lost their main attraction on the eve of the tournament, Naomi Osaka.
Maria Sharapova won 6-4, 4-6, 6-3 with the roof closed on Rod Laver Arena.
The pressure on the reigning French Open champion will only increase in her next round.
The Russian five-time Grand Slam champion was forced to stay up late in her second-round match.
The 31-year-old has only conceded three games en route to round three at Melbourne Park, where she won the title in 2008.
Roger Federer is working towards a third successive Australian crown and a 21st major victory.
Serena Williams is gunning to match Margaret Court's record of singles majors and claim an eighth Australian Open crown.
Kvitova has now lost both her matches and needs results to go her way in the White Group to stay afloat in the season-finale.
The 28-year-old Caroline Wozniacki had won the China Open in 2010.
Caroline Wozniacki and Angelique Kerber suffered shock defeats at the hands of less fancied opponents.
World number two Caroline Wozniacki and Wimbledon champion Angelique Kerber eased through their opening matches at the Wuhan Open in China on Tuesday.
Romania's Simona Halep continued to lead Women's Tennis Association (WTA) rankings released on Monday, ahead of Denmark's Caroline Wozniacki.
Hard work and peak fitness are the major concerns for world number two Caroline Wozniacki as she starts her first run to the US Open as a Grand Slam champion.
Caroline Wozniacki suffered fresh Wimbledon woe as the world number two suffered a shock 6-4, 1-6, 7-5 defeat against Ekaterina Makarova in the second round on Wednesday.
Novak Djokovic cruised through to the French Open second round in straight sets.
Simona Halep needed to reach at least the last eight and go further than world number two Caroline Wozniacki to retain the top-ranking going into the French Open.
Caroline Wozniacki says it would be "impossible" for her to follow Serena Williams' lead and return to tennis after giving birth.
Kasatkina recorded her second straight win over Wozniacki, having also beaten the reigning Australian Open champ at the St. Petersburg tournament last month.
