"I'm taking down numbers for everybody who sells food. Everybody. Because you can't compete [with] Amazon. They will not let you compete," Cramer said, noting the e-commerce giant can now "change the whole paradigm."
The deal is expected to close in the second half of the year. Whole Foods Chief Executive John Mackey will remain CEO of the grocery store chain, which will continue to operate under the Whole Foods brand.
Amazon opened its first New York City brick-and-mortar bookstore in late May.
On Thursday, Kroger shares plunged after the company cut its adjusted earnings forecast to $2.00 to $2.05 per share for the year ending January 2018, down from the $2.21 to $2.25 previously forecast.
— CNBC's Sarah Whitten and Reuters contributed to this report.