Free agent Brady confirmed on Tuesday that "my football journey will take place elsewhere", bringing an end to a glorious two-decade run in New England that included six Super Bowl titles.
Kraft was the owner when Brady was drafted with the 199th pick of the 2000 NFL Draft and he had said earlier this offseason that he hoped the 42-year-old either remained with the Patriots, or retired.
But Kraft will not get his wish, having spoken with Brady on Monday and being informed of his intentions.
FOREVER A PATRIOT pic.twitter.com/QSBOJBs4uy— Tom Brady (@TomBrady) March 17, 2020
"Tommy initiated contact last night and came over," Kraft explained to ESPN.
"We had a positive, respectful discussion.
"It's not the way I want it to end, but I want him to do what is in his best personal interest.
"After 20 years with us, he has earned that right. I love him like a son."
Brady added that he does not "know what my football future holds", though it is thought the Tampa Bay Buccaneers and Los Angeles Chargers will be among those keen to acquire the veteran quarterback in free agency.