Kruis played 57 minutes of England's win over Argentina, but is one of nine players released back to their clubs for Aviva Premiership action.
Kruis was viewed as a key member of the England team as recently as last year's Six Nations, but he has failed to maintain that progress and was dropped following an error-strewn performance in the first Test of the British and Irish Lions tour to New Zealand.
Marler returns after completing his three-week ban for striking with the elbow and will either start or be named on the bench against Australia, depending on whether Jones decides to reduce Mako Vunipola's workload.
Alex Lozowski has also been dropped despite appearing as a second-half replacement on Saturday, making the initial break that led to Semesa Rokoduguni's match-sealing try.
Tom Dunn, Piers Francis, Zach Mercer, Marcus Smith and Denny Solomona have all also returned to their clubs.
Ben Te'o will remain with the squad until Wednesday as the centre continues his recovery from an ankle injury, while Mike Brown is included in the squad despite landing on his head in a nasty fall against the 2015 World Cup semi-finalists last weekend.