"Moving forward, it's never easy to change -- especially when you work with great people like Rainer. But for now, we've decided that it's the right time for a fresh start," Kerber said on Twitter.
"He has become a friend and I'm thankful for his hard work and dedication in the last months."
Kerber's defence of her crown at the All England Club came to end in the second round at the hands of Lauren Davis, who had been ranked outside the top 250 earlier this year.
The former world number one, who also won the US and Australians Opens in 2016, has dropped to 13th in the WTA rankings after a poor season so far.
In addition to her Wimbledon disappointment, she was humiliated in straight sets by the unseeded Danielle Collins in the last 16 of the Australian Open and knocked out in the first round at Roland Garros.