The Wallabies refused to comment on the situation on Saturday night.
"I was bitterly disappointed to be honest, I'm on record with the referees' boss Alain Rolland about the treatment to our captain and to our players by Romain Poite and also by Nigel Owens over this last year," Cheika said after his side's 29-9 loss.
"I'm not quite sure why, but there was a time there in the game, in a break in play, where the national captain of Australia was asking the referee, 'When might be an opportunity for me to talk to you?' And he just absolutely ignored him.
"He's got the whistle, I understand, but there's a place where that guy, the captain, has an opportunity to speak to the referee.
"And the referee may not like the captain personally, that might be his prerogative, but he has to afford him that opportunity if he's affording it to his opponents.
"I don't know if it's subconscious or not, but it's there, it's got to be dealt with because that can't be going on.
"I don't know if they've got predetermined positions on our players, I asked Alain Rolland, I saw him last week in Sydney, and he said 'No, that's a surprise to me if that is'.
"But it's pretty blatant to anyone listening to the ref's ears."