Aegerter will join the previously-announced Remy Gardner in what will be an all-new line-up for the satellite Yamaha team.
The 31-year-old Swiss rider, a one-time race winner in Moto2, missed out on a graduation to WSBK last year despite a dominant title win in Supersport in 2021, staying in the secondary category for this season.
He leads the current standings by 36 points with four rounds to go, and already has one title to his credit this year in MotoE.
"I’m super happy to join Yamaha in the WorldSBK championship next season," said Aegerter. "It is a great opportunity for me, and a fantastic reward for the world championship title last year and for leading the WorldSSP series this year.
"I can’t wait for the first test aboard the Yamaha R1 as it’s clearly a competitive bike, with Toprak [Razgatlioglu] racing it to the world championship last year and in the title hunt once again this season.
"I am happy to have this opportunity, and I want to thank Yamaha and the GYTR GRT Yamaha team for believing in me. I will give it everything I have next season, but for now my focus is on securing a second successive world title in WorldSSP."
Aegerter and Gardner will replace GRT's current line-up of Garrett Gerloff and Kohta Nozane.
Gerloff is already confirmed to be moving to the Bonovo BMW team for 2023, while Nozane looks set to exit WSBK, with a return to the All-Japan Superbike Championship his most likely move.
Yamaha Europe Road Racing manager Andrea Dosoli added: "Ever since he entered the paddock, Dominique has shown that he is one of the top talents, and it was clear from very early on that he was ready for his WorldSBK chance.
"Unfortunately, there wasn’t an opportunity to give him that chance in 2022, but when a seat became available for 2023 then Dominique was the obvious choice to fill it.
"Not only has he impressed with his pace, race craft and consistency, but he’s also shown the determination and drive needed to be competitive at this level.
"He’s shown throughout his career that he’s able to adapt very quickly to new machinery, and we’re sure that this ability will pay dividends for him when he steps up to race the Yamaha R1 WorldSBK next season. We’re very much looking forward to seeing what he can do."