Prop Ellis Genge and back Alex Lozowski, who both came on as replacements against Argentina, have also been left out of the 25-party, although Harlequins loose-head Joe Marler and second row Charlie Ewels of Bath have been included.
Kruis, a peripheral figure in England's opening global of the autumn, has suffered a number of injury setbacks in recent times and was also dropped for an error-strewn performance in the first Test of the British and Irish Lions tour to New Zealand.
Bath's Charlie Ewels is named instead of Kruis while wing Jonny May is in contention after a hamstring injury.
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The 27-year-old, a protege of England forwards coach and his former Saracens captain Steve Borthwick, was viewed as an indispensable part of the team as recently as the RBS 6 Nations but his star continues to wane.
Lozowksi's exit means that his Saracens colleague Owen Farrell is nearly certain to be involved against the Wallabies after being rested for Argentina alongside Maro Itoje, who is also poised to make his comeback.
Mike Brown, who is completing his return to play protocols having suffered a concussion against Argentina, is one of the 25 players retained by Jones.
Elsewhere, Ben Te'o will remain in the camp until Wednesday before being released back to club side Worcester Warriors.
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