Joubert has been blamed for making a wrong call in penalising the Scots for being deliberately offside after a long lineout throw in the closing minutes of the game at Twickenham on Sunday.
The Wallabies, down 34-32, made the most of their reprieve with Foley keeping his nerve to kick three points and put his side through to a semi-final against Argentina.
"He (Joubert) gave it as a penalty. It's been pretty interesting to see how things have gone down. I've been really interested to see some of the rhetoric that's come out about officialdom over the week," Cheika told a news conference on Monday.
"I know that's the point that everyone's focussing on but no one's congratulating Joubert for picking up the tiniest knock-on before we scored the try in the corner and going back to the TMO.
"Some decisions you'll get and some decisions you won't. Everything in rugby is open to interpretation because everything in rugby is a contest. And that's the great thing about rugby; it's a contest sport."
Joubert sprinted off at the end of the match without shaking the hands of the players, but Cheika saw nothing unusual.
"Someone threw a bottle at him, didn't they? I'd be racing off too if I saw a bottle coming. I don't think anything of him going off quickly.
"I don't like the way that people are making something out of the way he ran off the field. You've got to assess the things for what they are and not the more romantic nature of what we're all thinking. He's just a person like everyone else."
Australia will face the Pumas on Sunday and picked up a fresh injury with prop Scott Sio, given a torrid time by the Scots in the scrum, having "very reduced motion" in his right elbow.
Cheika was more hopeful of loose forward David Pocock and fullback Israel Folau's return to fitness after they missed the Scotland game.
"Pocock ran yesterday pain-free, so he's looking more promising. Folau will run again tomorrow so I'd say it's more chance that they will play than they won't at this stage."
(Reporting by Justin Palmer, editing by Mitch Phillips)
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