The forwards were rocked by three-week bans for a tip-tackle on Samoa flanker Jack Lam, which saw him dropped on his head, and that has ruled both out of the remainder of the World Cup.
Scotland are pondering an appeal but it appears likely that both Ford and Gray will miss Sunday's quarter-final clash against the Wallabies at Twickenham.
In response to the news, Cheika said: "I haven't seen the incident but I feel for them. It's the World Cup, you have worked hard for it and when you get to possibly three finals to play, you miss out.
"The same happened to Michael Hooper last week. His grandparents came over to watch him play last weekend and he was suspended. I know it's a little thing but it's important. You feel for the players."
Despite the blow for Scotland, Cheika is still expecting a tough encounter against Vern Cotter's side regardless of what team is put out.
He added: "The guys who will replace those two are ready to roll. We understand there will be 23 players in the Scotland jersey trying to smash us. It doesn't matter the names on the jerseys."