The 59-year-old took to Instagram to share a gallery of photos of the former co-hosts together during their decade-long stint on the breakfast program, along with her best wishes for his future.
"Wishing @karlstefanovic_ all the best," she wrote. "Because when it was good, it was great..."
On Wednesday afternoon, Nine released a statement confirming that the network and Stefanovic mutually agree it was time for the 44-year-old to "step off" the show.
"For over 14 years Karl has been at the centre of the Today Show bringing his unique personality and perspective to the day's news and current affairs," Darren Wick, Director of News and Current Affairs, said.
"An announcement on the new line up and format of the Today Show will be made in the coming weeks."
Karl also thanked Nine in a statement.
"For the last 14 years I've co-hosted the best show on television. I can't thank Nine enough for the opportunity. I never in my wildest dreams thought I would be good enough to host this grand show for so long," he says.
It's rumoured that Wilkinson and Stefanovic's relationship soured after she left the program to join The Project in 2017 and she did not score an invite to his recent wedding to Jasmine Yarbrough.