"Sarah is in for Ally after testing positive for COVID-19," Karl said on Tuesday morning's show.
"Brooke has also come down with COVID-19. Both are in isolation and we will see them sometime next week."
Sarah Abo is now currently filling in for Ally, while Weekend Today's Richard Wilkins will be taking on Brooke's entertainment news as she recovers.
Meanwhile, Karl had a theory as to why he's managed to dodge the highly-transmissible virus as it continues to take down his colleagues.
"Interestingly, those of us who are elite athletes... are fine," Karl, who contracted COVID at the end of last year, joked.
A representative for Nine confirmed that both Brooke and Ally would be off until further notice, saying, "Both Ally and Brooke tested positive to Covid on Monday. They are both now isolating for seven days and will return back on air once they are clear and feeling better.
"Regular testing and observing any symptoms of those who have come into contact with them will continue."
It's thought the pair caught COVID after the Today show team attended Sony's annual Wharf4Ward cancer charity event in Sydney last Thursday.
It's the latest in a string of Australian breakfast TV figures coming down with the virus, with Sunrise star David 'Kochie' Koch revealing he had tested positive for COVID after attending the Red Cross flood appeal telethon on March 12 alongside a slew of Australian celebrities, which included Natalie Barr, Sylvia Jeffreys, and Carrie Bickmore.
Despite testing negative prior to his appearance on the program, Kochie said he had felt "shaggy" on Sunday - during which he tested positive for COVID.
“I tested negative on Saturday lunchtime ahead of the Australia Unites broadcast but then woke up feeling a bit shaggy on Sunday morning, which I initially put down to the late finish and sharing the bottle of red wine that Sylvia and Dr Chris insisted we share (that’s my version and I’m sticking with it),” he said in a statement.'
“But then I tested again and it came in positive. Symptoms are mild and I’m following the health orders.”