Czech second seed Kvitova, who also won the 2011 title, lost 3-6, 7-5, 6-4 to veteran campaigner Jelena Jankovic who goes on to play 2012 runner-up Agnieszka Radwanska for a spot in the quarter-finals.
Kvitova’s earliest loss at the All England Club since 2009 leaves just Serena Williams, Maria Sharapova, Caroline Wozniacki and Lucie Safarova as the last remaining top 10 seeds going into the second week.
“I’m overwhelmed. I’m so excited. My heart is still pumping,” said the 30-year-old Jankovic on reaching the last 16 for the fifth time.
Kvitova has now bowed out of the last four Grand Slams before the quarter-finals.
“It’s not great to lose in the third round. Not to be in the second week of the favourite tournament for me is really sad,” she said.
Seven-time champion Roger Federer defeated big-serving Australian Sam Groth 6-4, 6-4, 6-7 (5/7), 6-2.
The 33-year-old Swiss, chasing an 18th major title, will next face Spanish 20th seed Roberto Bautista Agut.
Groth had the consolation of hitting the second fastest serve ever at the tournament — 147.2-miles (236.9-kilometres) per hour.
Murray faces golden oldie
Murray survived a shoulder injury scare to make the last 16 with a 6-2, 6-2, 1-6, 6-1 win over Italy’s Andreas Seppi.
Murray, the 2013 champion, required a medical time-out for treatment on his right shoulder after dropping the first game of the fourth set.
But the world number three then reeled off six games in succession to set up a clash against Croatian giant Ivo Karlovic on Monday for a place in the quarter-finals.
“The shoulder is fine. The trainer came out and manipulated my back. He gave it a few good cracks,” said Murray.
“It’s a 90-kilo guy lying on top of me so it’s not that pleasant. He said the shoulder was like a machine gun going off when he laid on top of me.”
Karlovic became the oldest man in 39 years to reach the last 16 when he beat French 13th seed Jo-Wilfried Tsonga.
The 36-year-old giant fired 41 aces in a 7-6 (7/3), 4-6, 7-6 (7/2), 7-6 (11/9) win.
The 2010 runner-up Tomas Berdych, the Czech sixth seed, saw off Spain’s Pablo Andujar 4-6, 6-0, 6-3, 7-6 (7/3).
He next faces Gilles Simon who beat Gael Monfils 3-6, 6-3, 7-6 (8/6), 2-6, 6-2.
Their all-French clash started on Court One but was completed at 10:30pm (2130GMT) under the roof and lights of Centre Court after darkness fell.
Dreadlocked German qualifier Dustin Brown was unable to follow his triumph over Rafael Nadal when he slumped to a 6-4, 7-6 (7/3), 4-6, 6-3 defeat to Serbian 22nd seed Viktor Troicki.
Qualifier Brown joins Lukas Rosol, Steve Darcis and Nick Kyrgios who all lost their next match at Wimbledon after knocking out Nadal over the last four years.
Troicki goes on to face Canada’s Vasek Pospisil, who beat British wildcard James Ward 6-4, 3-6, 2-6, 6-3, 8-6.
It is the 29-year-old Serb’s first last-16 run at Wimbledon since 2012 and his best performance at a Grand Slam since returning from a 12-month drugs ban in July last year.
US Open champion Marin Cilic took just two games to see off John Isner on Saturday after returning to finish their third round match poised at 10-10 in the final set.
Croatian Cilic, the ninth seed, beat the US 17th seed 7-6 (7/4), 6-7 (6/8), 6-4, 6-7 (4/7), 12-10 in a match that lasted four hours and 31 minutes in total after it had been suspended late Friday due to bad light.
Cilic next faces wildcard Denis Kudla, the last American man in the tournament.
Danish fifth seed Wozniacki reached the last 16 for the fourth time with a comfortable 6-2, 6-2 win over Italy’s Camila Giorgi.
The former world number one will face Spain’s Garbine Muguruza after the 20th seed shocked 2012 semi-finalist Angelique Kerber 7-6 (14/12), 1-6, 6-2.
Muguruza saved nine set points in the first set on her way to a debut appearance in the second week at Wimbledon.
Romania’s Monica Niculescu also made the last 16 for the first time, beating Czech world number 134 Kristyna Pliskova 6-3, 7-5.
She will face Switzerland’s Timea Bacsinszky who put out 2013 runner-up Sabine Lisicki 6-3, 6-2 to book a spot in the last 16.
Belarusian qualifier Olga Govortsova is another fourth round first timer thanks to a 7-6 (7/4), 6-3 over Magdalana Rybarikova.
She next tackles American 21st seed Madison Keys, a semi-finalist in Australia this year.