Kerber looked mightily relieved after saving her world number one status in a tense 4-6, 7-6 (7/2), 6-4 win over US world number 70 Shelby Rogers.
The German star was a break down in the second set but did just enough to claw her way into Monday's fourth round where she will face Garbine Muguruza.
Agnieszka Radwanska, Svetlana Kuznetsova, Coco Vandeweghe, Magdalena Rybarikova and qualifier Petra Martic also won their third round ties.
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.
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- One-game wonder -
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Querrey and Tsonga's match was called off at 6-2, 3-6, 7-6 (7/5), 1-6, 6-5, with the French 12th seed not wanting to serve as the light faded, though Querrey was happy to receive.
They returned to finish the contest on Saturday but it was all over in a matter of minutes as the US 24th seed broke serve.
Querrey said: "It's really the most anti-climactic way to finish a match."
He faces South Africa's Kevin Anderson for a quarter- final spot.
Bulgarian 13th seed Dimitrov had an easy ride into the last 16 when Israeli Sela was forced to pull out at 6-1, 6-1 down after struggling with a right thigh injury that required treatment during the match.
The 2008 Wimbledon junior champion will next face meet either Federer or Mischa Zverev.
Canadian sixth seed Milos Raonic, last year's beaten finalist, downed Spain's 25th seed Albert Ramos-Vinolas 7-6 (7/3), 6-4, 7-5 to book a fouth round spot against either Alexander Zverev or qualifier Sebastian Ofner.
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Muguruza stepped up her bid to return to the Wimbledon final with a 6-2, 6-2 victory over Romania's Sorana Cirstea.
The world number 15 became the first Spanish woman to reach the All England Club title match in 19 years when she was beaten by Serena Williams in the 2015 final.
"Every time I start the grass season, I'm like, 'How the hell did I reach that final?'," the 2016 French Open winner said.
An off-sorts Cirstea had witnessed the horrific knee injury suffered by her opponent Bethanie Mattek-Sands in the previous round on Thursday.
"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.
"I have had lots of injuries in my career but this is definitely the worst.
"I will be out for a while but I will get through this."
- Radwanska digs deep -
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The deft Radwanska, who lost the 2012 final to Serena Williams, came back from a set down to beat Swiss 19th seed Timea Bacsinszky 3-6, 6-4, 6-1 on Centre Court.
Radwanska next faces Russian eighth seed Kuznetsova, the 2004 US and 2009 French Open champion, who cruised through with a 6-4, 6-0 win over Slovenian qualifier Polona Hercog.
"I am a little disappointed as I didn't keep my level up throughout the whole match but if you had said I would make the third round of the main draw I would have been happy," Hercog told AFP.
Vandeweghe, considered by some as a dark horse for the title, beat compatriot Alison Riske 6-2, 6-4. She next faces Caroline Wozniacki or Anett Kontaveit.
She next faces Rybarikova, who eased into the last 16 of a major for the first time with a 6-2, 6-1 win over Lesia Tsurenko of Ukraine.