Auer was set to partner Daniel Juncadella and Nicky Catsburg in Craft-Bamboo Racing's all-Pro Mercedes AMG for the Intercontinental GT Challenger opener next Sunday.
That was until the 2022 DTM runner-up was ruled out of both the Daytona 24 and the Bathurst 12 Hour after suffering broken vertebrae in a nasty crash during practice on Thursday.
That left Craft-Bamboo looking for a last-minute replacement for Bathurst, the team ultimately landing on factory Mercedes driver Ellis.
The 30-year-old German, who won a DTM race at the Lausitzring in 2021, was challenging for a second Daytona win in Winward's replacement chassis following Auer's accident when he was involved in a clash with the factory GTD Pro Corvette in the closing stages and clipped the same wall the Austrian had struck.
"Philip Ellis will replace Lucas Auer in the #77 Mercedes AMG Team Craft-Bamboo [entry] for the Bathurst 12 Hour, starting February 3," posted Mercedes-AMG Motorsport on Twitter.
"We continue to wish Luggi a fast recovery!"
Auer posted on social today for the first time since his accident. Accompanying a video showing him walking with the support of a frame, he wrote: "Guys, thank you so much for all the love and messages. My surgery went very well and I‘m doing good.
"Also a big thank you to the amazing medical team for taking such great care of me. I am ready for the next steps of rehab and looking forward to seeing all of you at the track soon."
Ellis joins a host of Mercedes factory and affiliated drivers that will make the trek down under for the 12 Hour this week.
Daytona 24 GTD Pro winners Juncadella, Maro Engel and Jules Gounon will all race at Mount Panorama, spread across separate entries.
Juncadella will be in the Craft-Bamboo car while Engel will join Mikael Grenier and Raffaele Marciello in the GruppeM AMG.
Gounon, meanwhile, will return to SunEnergy1 Racing as he looks to win a third straight Bathurst 12 Hour, following his triumphs with Bentley in 2020 and then with Kenny Habul's Mercedes squad in 2022.
Maximilian Gotz, meanwhile, will join local stars Shane van Gisbergen and Broc Feeney in Triple Eight's all-Pro AMG.
The 2023 Bathurst 12 Hour kicks off with practice starting this Friday.
Watch all of the Bathurst 12 Hour action on Motorsport.tv (not available to viewers in Australia or New Zealand).