Loosehead prop Ross, linked up with the squad in July, while scrumhalf Thomas was in camp with the team in Perth where he spent valuable time with the recently retired Nic White.
Playmaker Carter Gordon has been selected, having been announced as returning to Australian Rugby with the Queensland Reds in a long-term contract. The 24-year-old made his Wallabies debut in Pretoria in 2023 and went on to start at flyhalf in five of eight Tests in his first year of international rugby, including two matches at the Rugby World Cup.
Western Force flyer Dylan Pietsch returns to the group after a period on the sideline recovering from a fractured jaw, while fellow outside back Andrew Kellaway is also selected after a calf strain ruled him out of the latest two Wallabies Tests against New Zealand.
Australia A squad members Matt Faessler, Josh Canham, Pete Samu and Hamish Stewart have also been named and will link up with the Wallabies in Tokyo after the match against Japan XV in Osaka on October 18.
Elsewhere, the squad remains mostly consistent with the group that has featured so far throughout the 2025 Test season.
Overseas-based players may link up with the group, but not during the first two matches of the Tour, due to those matches falling outside the World Rugby Regulation 9 window.
The Wallabies will play five consecutive Tests on their End of Year Tour against Japan in Tokyo, England in London, Italy in Udine, Ireland in Dublin and France in Paris. It will be the first time the Wallabies have played in Japan since 2021 and Italy since 2022.
The squad, which is comprised of 19 forwards and 15 backs, will assemble in Sydney on Thursday evening, where they will train and attend the Rugby Australia Awards on Friday, before departing for Tokyo.
"The squad and staff have had a brief chance to catch their breath after what has been a dense and attritional Test season so far," said Wallabies coach Joe Schmidt.
"The challenge certainly doesn't get any easier with five consecutive Tests on the road against high-quality international opposition but, in saying that, I think the squad will relish the challenge and players will work hard to be as competitive as possible.
"Both Aidan Ross and Kalani Thomas have had a bit of time with us and Carter Gordon will get the opportunity to integrate back into the Wallabies environment. The three players are fully fit and eager to be involved.
"We've taken a long-term view with Tom Lynagh, who is still just 22-years-old. He has had a few injury frustrations since the third test versus the Lions in early August and will follow an individualised program, guided by both Wallabies and Queensland staff, which will allow him to recover to full fitness.
"There are a few players who have featured during recent Test matches, that are currently involved in competitions in Europe. Given the intensity of our Tour schedule, we may look to bolster our playing stocks by including some of these players during the World Rugby Regulation 9 window."
Wallabies squad
Forwards
Allan Alaalatoa, Angus Bell, Josh Canham, Nick Champion De Crespigny, Matt Faessler, Nick Frost, Fraser McReight, Josh Nasser, Zane Nonggorr, Billy Pollard, Tom Robertson, Aidan Ross, Lukhan Salakaia-Loto, Pete Samu, Carlo Tizzano, Taniela Tupou, Rob Valetini, Jeremy Williams, Harry Wilson (c).
Backs
Filipo Daugunu, Tane Edmed, Josh Flook, Carter Gordon, Jake Gordon, Max Jorgensen, Andrew Kellaway, Ryan Lonergan, Hunter Paisami, Dylan Pietsch, Harry Potter, Hamish Stewart, Joseph-Aukuso Suaalii, Kalani Thomas, Corey Toole.