Stefanovic said, 'It all came as a bit of a shock to us yesterday,' and also told the audience he would address it in a later segment.
According to a statement released by Channel Nine, the TV network were 'unable to meet the expectations' of Wilkinson.
Wilkinson's departure from the network comes as The Sunday Telegraph released explosive reports the 57-year-old television host was holding out on re-signing with the network until she was granted 'pay-parity' with Stefanovic.
Wilkinson has been hosting the popular morning show, alongside Karl Stefanovic, for just over 10 years.
The move from the veteran journalist and TV presenter is being praised as a landmark victory for women in television.
Now, Channel Ten has announced it has successfully signed Wilkinson to host The Project. In a statement, the network said more roles for Wilkinson would be announced in the coming months.
Although Karl is believed to have not known of Lisa's plans to abruptly leave the show, looking back at last night's episode of Today some have noticed the host took a subtle swipe at Wilkinson.
Interviewing The Block's Darren Palmer and Neale Whitaker towards the end of the show, Stefanovic began to wrap the interview up: 'The Block continues at 7:30 on Nine...and we're so glad it is,' he said with a smile.
Brushing off what now appears to be a big tell, Lisa simply laughed and said: 'Don't be silly.'
Stefanovic is yet to make a formal statement.
This article originally appeared on New Idea.