Cherry suffered a concussion after slipping on the stairs at the hotel on Monday, Scottish Rugby said, and the team took the decision to replace him in the squad for the rest of the tournament.
McInally had already been on standby following a concussion suffered by Ewan Ashman last week, Scottish Rugby added.
Scotland next play Tonga on September 24 in Nice, looking to bounce back from their opening round defeat by South Africa.
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