Bosses were plunged into a last-minute shake-up after Motsi was forced to self-isolate at home following an "urgent" trip to Germany.
As a result she will not be in the studio for at least two weeks until her quarantine period is over, missing the next couple of live shows.
And it seems the first choice for execs was to have Anton replace her, given his extensive professional dance background and familiarity with the show.
In a statement, the show said: "We are pleased to announce that the King of Ballroom Anton du Beke is stepping into our Judging panel this weekend.
"Good luck Anton!"
It added: "News: Anton has a new role on?#Strictly?this weekend!"
Bosses plan to temporarily promote dancer Anton to the judging panel after years of speculation he could step up.
Motsi took to Twitter to update fans on Thursday, writing: "Hi Guys - Earlier this week I needed to travel to Germany for an urgent reason."
Motsi is still set to appear on the show virtually, but will be absent from the studio like fellow judge Bruno Tonioli, who is still in America.
She added: "I will of course be following the UK Government guidelines and self-isolating for 14 days. I'll be watching from home and by the power of technology, should be in your living rooms.
"Watch out though, I'll be doing my own hair and make-up!"
A spokesman told Mirror Online: "Motsi had to make an essential journey and will now be isolating for 14 days as per government guidelines.
"We look forward to welcoming her back to the Strictly studio in a few weeks."
It comes as Katya Jones and Nicola Adams were forced to quit the series today, after Katya tested positive for coronavirus.
Nicola has tested negative, while she must stay in quarantine for 14 days as she has been in direct contact with Katya.
It Takes Two host Rylan Clark-Neal is also self-isolating, after coming into contact with someone with the virus.
Gethin Jones has replaced Rylan on the show until he returns, while no one will replace Katya and Nicola.
* Strictly Come Dancing continues on Saturday on BBC One.
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