World No.1 Barty won 6-2 6-4 against French Open champion Barbora Krejcikova, whom she also defeated in the fourth round during her Wimbledon title run last month.
Kerber and Kvitova then battled it out for the right to tackle Barty in the last four, but a quarter-final that was building momentum ended prematurely when two-time Wimbledon winner Kvitova found a recent stomach problem too troublesome.
Kerber was 6-4 3-3 ahead in the contest, having recovered from being an early break down in the second set, getting her game together as 31-year-old Kvitova began to suffer.
During an injury timeout, which Kvitova called after the fifth game of the second set, the Czech received a massage to her abdominal region and played on briefly, before walking up to the net to concede the match.
It remains to be seen whether the setback in Cincinnati might have consequences for her involvement at Flushing Meadows, with the US Open due to begin on 31 August (AEST).
Kvitova wrote on Twitter minutes after coming off court: "I stayed out there as long as I could. I have been struggling with a stomach issue for several days and unfortunately couldn't finish the match today. Good luck Angie - sorry to end it that way - and can't wait for the next battle with you."
I stayed out there as long as I could.— Petra Kvitova (@Petra_Kvitova) August 20, 2021
I have been struggling with a stomach issue for several days and unfortunately couldn’t finish the match today.
Good luck Angie - sorry to end it that way - and can’t wait for the next battle with you 😘#CincyTennis pic.twitter.com/EJA3XmFcYm
Kerber said: "Of course, this is not the way you would want to win the match. I hope Petra will recover as fast as possible and be ready for the US Open.
"I know she's a big fighter and fights until the last points, so I hope she is not too bad and hope she is fine really, really soon."
Kerber has now won 14 of her past 15 matches, with the exception being her Wimbledon semi-final defeat to Barty.
Barty got through in a more routine manner on Friday, albeit having to battle from a break down in the second set against the fast-rising Krejcikova, who has shot up from No.65 in the world to a career high of No.10 this year.
Barty said: "Barbora served exceptionally well early in that second set and was able to take advantage of a service game of mine where I just hit too many second serves.
"I wanted to try and get a little bit more positive on her service games and then try to get myself in the points a little bit more. I'm happy to run away with that one in the end."