The Saracens lock, who earned his 21st cap in the Red Rose's 21-8 win over Argentina at the weekend, is one of a number of players to drop out.
Prop Ellis Genge and back Alex Lozowski are also overlooked for selection, with Joe Marler coming in for the former and Jonny May back in contention to feature at Twickenham after overcoming a hamstring injury.
Charlie Ewels will take over from Kruis in the squad to face the Aussies, meanwhile, as Jones - who will confirm his final matchday 23 on Thursday morning - looks for an improved performance in the second of the November matches.
Elsewhere, Ben Te'o will remain in the camp until Wednesday before being released back to club side Worcester Warriors.
Players released back to their clubs:
Tom Dunn (Bath Rugby), Piers Francis (Northampton Saints), Ellis Genge (Leicester Tigers), Nick Isiekwe (Saracens), George Kruis (Saracens), Alex Lozowski (Saracens), Zach Mercer (Bath Rugby), Marcus Smith (Harlequins), Denny Solomona (Sale Sharks)