Williams has had an exceptional season to date, reaching the finals of the Australian Open and Wimbledon.
Kvitova, meanwhile, who returned to the women’s circuit just six months after she was stabbed in the hand of a knife attack, was thwarted by the former champion.
The left-hander, who knocked out Wimbledon champion Garbine Mugurza in the fourth round, was unable to stop the American.
Williams, who had been involved in a lot of three-setter matches at Flushing Meadows, needed three sets again, but prevailed 6-3, 3-6, 7-6 (7-2).
Kvitova was aggressive from the off, attacking Williams’ serve.
The pressure seemed to tell early on, as Williams made a double fault which enabled Kvitova to break.
Williams was solid with her groundstrokes and ultimately that proved telling in the opener.
Kvitova came firing in the second and while a short rain delay halted proceedings, it didn’t stop her momentum.
Her serves were unerringly accurate and she levelled the match up.
The decider swung one way and then the other.
Kvitova looked to be heading to victory when she opened up a -2 lead in the final set.
But after going to tie-breaker, Williams took full control.
Despite throwing away her first match point with a double fault, she took the second when Kvitova misfired with her return.
More to follow