The defending champion was toppled by a muscular performance by Williams, to set up a semi-final showdown with Victoria Azarenka.
Azarenka and Williams set for Wimbledon semi-final clash
The 30-year-old dismissed the defending Czech 6-3 7-5 on Centre Court to muscle her way through to a mouthwatering semi-final clash against Victoria Azarenka.
The 30-year-old American used her powerful serve to great effect in the match, sending down 13 aces and winning 86% of her first-serve points in her best performance in the tournament so far.
And afterwards revealed a pre-match talk from her dad and sister had played a key role in firing her up for the match.
"I had a good talk with my dad, he motivated me, and my sister as well," Williams said.
"I had a talk with Patrick (Mouratoglou - Williams' coach) too. It was great. All three of those got me really motivated to do better and be the player that I know I can be.
"I just took to heart what everyone said. I really prayed about it, just to have calmness of mind and just go forward and do the best I can do, whether that's winning or losing."
Kvitova admitted Williams is now her pick to win the championship following her dominant display.
"I think so," the 22-year-old said, when asked if Williams was now the tip to win the tournament.
"I think I didn't play badly, but she just served very well and that was the big difference.
"I think it's really tough to beat her."
Meanwhile, Azarenka saw off Tamira Paszek thanks to a second set tie-break after the Austrian fired long on match point to win 6-3 7-6 (7/4).
Azarenka said: "The games were really close. At the beginning of the second set we were really holding our serves well.
"It was a close match and there were a lot of long rallies but I'm glad I could manage to win.
"It's a great feeling to be in the semi-final of a grand slam but I still want to go all the way and it still seems so far away.
"There's no better opponent than Serena in the semi-finals so I'm really looking forward to that match."
Eighth seed Angelique Kerber booked her place in the last four with a hard-fought win over fellow German Sabine Lisicki.
Kerber claimed a 6-3 6-7 (9/7) 7-5 win over Maria Sharapova's conqueror after two-and-a-half hours to reach her first Wimbledon semi-final.
It was a roller-coaster battle, and Kerber looked like she had blown her chance when she missed three match points in the second set and then trailed 5-3 in the decider.
But Lisicki faltered when serving for the match and eighth seed Kerber reeled off four games in a row to triumph under the Centre Court roof.
In the other rain-affected quarter-final, Agnieszka Radwanska and Maria Kirilenko finished off the last few games of their match under the roof on Centre Court.
The match was suspended on Court One due to failing light at quarter to eight, with Kirilenko marginally ahead in the third set, 5-7 6-4 4-4 15-0.
However, after the break, Radwanska powered ahead to win 5-7 6-4 7-5 to set up a semi-final clash against Kerber.
The Polish number three seed will become world number one if she wins the title and rival Azarenka is knocked out at the semi-final stage.
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