"I remember I heard a pop in my leg and everything went slow after that", the American said Saturday from her hospital room in Wimbledon.
Kerber lost to Serena Williams, absent while she prepares for the birth of her first child, past year in the final at Wimbledon but was looking to avoid a repeat her 2015 performance by exiting in the third round this time around.
A third former finalist, Agnieszka Radwanska, the ninth seed from Poland, also needed three sets to beat Timea Bacsinszky.
"It definitely was a tough match, but I'm happy the way I fought", said Wozniacki. "I don't want to have any five-set matches".
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Again in the third set, Rogers appeared to be in a good position as she recovered from a first-game service break and battled to a 3-2, break-point advantage against Kerber.
After winning the Australian and U.S. Opens a year ago, Kerber has endured a miserable time in 2017, culminating in an embarrassing French Open first round loss to Ekaterina Makarova last month.
At 37, she is the oldest player left in the women's draw.
Seventh seed Svetlana Kuznetsova of Russian Federation eased through with a routine 6-4, 6-0 victory over Slovenia's Polona Hercog.
Djokovic will next face Adrian Mannarino, who defeated fellow Frenchman and No. 15 seed Gael Monfils 7-6 (3), 4-6, 5-7, 6-3, 6-2 in three hours, 30 minutes. Radwanska was the runner-up at the All England Club in 2012 to - yes, that's right - Serena Williams.
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Djokovic will next play Latvian Ernests Gulbis, who beat Argentina's Juan Martín del Potro 6-4, 6-4, 7-6 (7-3).
Canada's sixth-seeded Milos Raonic, last year's runner-up at Wimbledon, advanced to the second week by beating 25th-seeded Albert Ramos-Vinolas of Spain 7-6 (3), 6-4, 7-5.
The top-ranked Kerber has lost her past four matches against Muguruza.
The top seed was forced to play on Court 2 on Saturday but refused to make a fuss, despite no men's world No.1 having been seen anywhere but Centre Court or Court 1 this century. Sam Querrey took one game to beat Jo-Wilfried Tsonga in a match suspended Friday due to bad light, while Grigor Dimitrov made it through after opponent Dudi Sela pulled out-the 11th retirement at the championships.
Kerber was the first to blink in the match as Flipkens mixed up some powerful baseline hitting with a series of well-disguised drop shots to force a break in game six. They meet Monday for a spot in the quarterfinals.
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