Co-host Eddie McGuire will be steering the ship without the help of the embattled Today host in Friday's episode of The Long Weekend radio show.
The weekly news, sport and entertainment show was launched in June on radio giant ARN's Gold station and set to stream on Nine platforms.
It is understood Stefanovic backed out Friday's broadcast of his own accord and his future with the company is not in question.
But ARN will seek assurances from Stefanovic's management about plans for his independent podcast, The Karl Stefanovic Show, following a recent interview with UK anti-Islam figure Tommy Robinson.
Stefanovic has been criticised for failing to challenge Robinson during the near hour-long interview, which was released on Tuesday and deleted by Wednesday morning.
During the episode, Stefanovic praises the far-right activist's tenacity and courage for "trying to stand up for what you believe is right".
The podcast is run independently of Nine and ARN.
The episode reportedly sparked crisis talks at Nine, where Stefanovic serves as the co-host of its flagship breakfast program, Today.
Focus shifted to ARN after Nine reportedly decided to cut ties with Stefanovic.
While Nine has yet to confirm his departure, it took pains to distance itself from the podcast.
"Nine has no involvement, including in the guest selection and other editorial processes," a spokesperson told AAP on Wednesday.
"However, Nine is taking this matter seriously."
ARN has also put itself at arm's length, telling AAP its association with Stefanovic is limited to specific radio engagements.
"His external media activities, including his podcast, are undertaken in a personal capacity and are entirely separate from the network, which we have no control over," it said.
"They do not represent ARN's views, editorial standards or programming."
Prime Minister Anthony Albanese also weighed in on the matter, suggesting Stefanovic had moved further and further out on the edges of what is mainstream political debate in this country.
"I think that that can have an impact (on social cohesion)," he told an event in Canberra.
The Karl Stefanovic Show episode went live on Tuesday evening and was scrubbed across multiple platforms by Wednesday morning.
It is unclear why Stefanovic's interview with Robinson was taken down or who made the call.
One Nation leader Pauline Hanson reposted video of the episode on her YouTube channel on Wednesday, claiming Nine was trying to sack her good friend.
The interview sparked a rebuke from activist group Mad F***ing Witches, a grassroots group that has previously drained advertising revenue from ARN over its employment of shock jock Kyle Sandilands.
Robinson, whose real name is Stephen Yaxley-Lennon, co-founded the now-defunct anti-Islam English Defence League movement.
He has twice cancelled speaking tours of Australia after being denied a visa and has multiple criminal convictions.
Nationals leader Matt Canavan also rushed to Stefanovic's defence once news broke he was expected to depart Nine.
"Australian journalists should not lose their jobs for talking to someone," he wrote on X.
In a video teasing the episode online, Stefanovic puts his arm around Robinson.
"I really do admire your tenacity and the courage that you're showing in trying to stand up for what you believe is right," he said during the interview.
Stefanovic, who has co-hosted Today on and off for more than two decades, has not responded to requests for comment.
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