Ollie Chessum and George Furbank are also set to miss Saturday's match in London, prompting Borthwick to call up Noah Caluori and Max Ojomoh from the England A squad for the Nations Championship clash.
Wing Feyi-Waboso, a standout performer in Sunday's win, suffered a right ankle injury from a hip-drop tackle by Australia's Angus Bell and will miss the rest of the tournament, British media reports said.
Flanker Tom Curry, who had missed the Australia test with a hip injury, is also out of the remaining Nations Championship matches.
Centre Atkinson will go into rehabilitation after suffering a hip injury in the 64th minute, England Rugby said on Monday.
Scrum-half Archie McParland has recovered from a calf issue and replaced Harry Randall in the squad.
England sit second in the Northern Hemisphere table, two points below France, with two group matches left.
Nations Championship 2026
The inaugural Nations Championship will see six northern hemisphere and six southern hemisphere nations battle it out across six rounds in the July and November international windows before assembling in Twickenham for one unforgettable finals weekend on November 27-29.
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England training squad:
Forwards: Fin Baxter, Arthur Clark, Alex Coles, Luke Cowan-Dickie, Ben Curry, Theo Dan, Ben Earl, Greg Fisilau, Jamie George, Ellis Genge, Joe Heyes, Max Hicks, Maro Itoje, Emmanuel Iyogun, Jack Kenningham, George Martin, Asher Opoku-Fordjour, Tom Pearson, Henry Pollock, Will Stuart
Backs: Noah Caluori, Fraser Dingwall, Tobias Elliott, George Ford, Tommy Freeman, Will Joseph, Joe Marchant, Cadan Murley, Archie McParland, Max Ojomoh, Henry Slade, Fin Smith, Marcus Smith, Ben Spencer, Freddie Steward, Jack van Poortvliet