The selection has been heavily shaped by injuries at scrum-half after Northampton's Alex Mitchell sustained a hamstring injury playing against Gloucester at the weekend and has been ruled out, along with teammate Archie McParland, who is dealing with a calf issue.
In their place, Bath's Ben Spencer and Bristol's Harry Randall have been called up to provide cover and competition at number nine.
Borthwick has retained a strong core of experienced players, with Saracens lock Maro Itoje set to captain the side.
The squad features 20 forwards and 16 backs and includes Northampton fly-half Fin Smith, who has been included despite missing the recent three-day training camp at Pennyhill Park. George Ford and Marcus Smith remain available as additional options at fly-half.
Wing Immanuel Feyi-Waboso has also been selected despite lingering fitness concerns, while Gloucester centre Seb Atkinson has passed a fitness test to earn his place in the group.
"These fixtures take on added significance this autumn as they represent our final opportunity to face southern hemisphere opposition before next year's Rugby World Cup," Borthwick said.
England will follow the Australia Test with home matches against Japan on 14 November and New Zealand on 21 November, before contesting the Nations Championship finals weekend later in the month.
England Nations Championship squad:
Forwards: Fin Baxter (Harlequins), Ollie Chessum (Leicester Tigers), Arthur Clark (Gloucester), Alex Coles (Northampton Saints), Luke Cowan-Dickie (Sale Sharks), Ben Curry (Sale Sharks), Tom Curry (Sale Sharks), Theo Dan (Saracens), Ben Earl (Saracens), Greg Fisilau (Exeter Chiefs), Jamie George (Saracens), Ellis Genge (Bristol Bears), Joe Heyes (Leicester Tigers), Maro Itoje (Saracens, captain), Emmanuel Iyogun (Northampton Saints), George Martin (Saracens), Asher Opoku-Fordjour (Sale Sharks), Tom Pearson (Northampton Saints), Henry Pollock (Northampton Saints), Will Stuart (Bath).
Backs: Seb Atkinson (Gloucester), Fraser Dingwall (Northampton Saints), Immanuel Feyi-Waboso (Exeter Chiefs), George Ford (Sale Sharks), Tommy Freeman (Northampton Saints), George Furbank (Harlequins), Will Joseph (Gloucester), Joe Marchant (Sale Sharks), Cadan Murley (Harlequins), Harry Randall (Bristol Bears), Henry Slade (Exeter Chiefs), Fin Smith (Northampton Saints), Marcus Smith (Harlequins), Ben Spencer (Bath), Freddie Steward (Leicester Tigers), Jack van Poortvliet (Leicester Tigers).
The squad assembles at England's performance centre at Pennyhill Park this week as Borthwick and his coaching team begin final preparations for what promises to be a demanding and high-stakes autumn campaign.
Italy coach Gonzalo Quesada believes Rassie Erasmus has shown his side great respect by selecting a near full-strength Springbok team for Saturday's Nations Championship clash in Turin.
Spain coach Luis de la Fuente has included three new faces in his squad for the final UEFA Nations League group-stage matches against the Czech Republic and England.
Thomas Tuchel has left Cole Palmer, Phil Foden and Kobbie Mainoo out of his latest England squad, while Jobe Bellingham and Fulham midfielder Josh King have received their first senior international call-ups.
The Springboks will put their No 1 ranking on the line when they face Italy in Turin on Saturday.
