Kerber was in action against Madison Keys and advanced courtesy of the American's retirement in Osaka.
Keys had pegged the German back by winning the second set but then succumbed to injury having been broken at the start of the third, down 6-4 4-6 2-1 when she called time.
Kerber said: "It was a really good match in the first two sets and this is never the way that you want to win the match.
"I hope Madison will recover really soon so she is ready for the next tournaments.
"I tried to give everything I could today and I'm looking forward to playing the next round."
However, the three-time grand slam champion was still waiting to learn the identity of her last-four opponent after the weather intervened.
Anastasia Pavlyuchenkova broke for a 2-0 lead over Misaki Doi in the opener before the rain started to fall, suspending the match for several hours before it was put back to Sunday (AEST).
Hometown hero Naomi Osaka, the former world No.1, did not get on the court at all against Yulia Putintseva. Elise Mertens was also made to wait to take on Camila Giorgi.