World Rugby issued a statement on Monday confirming it had reviewed the decision and agreed that Joubert had made a mistake in awarding the penalty, which Australia kicked to win the match 35-34, instead of a scrum.
Cheika, who has had a series of highly-publicised disputes with referees over the years, told reporters on Tuesday that he hoped other referees would stand by Joubert.
“I did feel for him. It is a bit surprising because no other decision in the tournament has been reviewed," Cheika said.
“I really feel for the ref. I genuinely feel for him. It is so unfair. No other referee has had his stuff put out there like that and Craig Joubert is a very good referee.
“Genuinely I have never seen that before. I am not sure why that decision had to be publicly reviewed and put out there. I really hope his fellow referees stand by him."
Joubert awarded Australia a last-minute penalty when Scotland knocked on at a lineout and Jon Welsh caught the ball in an offside position.
But television replays showed that Australian scrumhalf Nick Phipps touched the ball just before Welsh, so the Wallabies should have been awarded a scrum rather than a penalty.
Joubert was initially criticised for not referring the incident to the television match officials but World Rugby confirmed that under tournament rules, he was not permitted to ask for a review.
"Unfortunately in this instance, people have taken the game off the field and gotten quite personal about it," Cheika said.
"Supposedly, these are big people in the game who are earning their living from the game through commentary and stuff like that.”
Scotland are not the first team to be knocked out of the World Cup after a controversial decision.
In the inaugural Rugby World Cup in 1987, Australia lost to France in the semi-finals after Serge Blanco scored a spectacular late try after the ball had been knocked on in the lead-up.
In 2007, France knocked New Zealand out of the World Cup quarter-finals after being awarded a critical try off a forward pass that was missed by the referee.
Cheika has been highly critical of referees.
Last year he was given a suspended six-month ban and fined for abusing a cameraman in South Africa. He was also fined after abusing match officials during and after Stade Francais' loss to Harlequins in the 2011 final of a European competition.
“I can't make it sound like I'm looking after the referee because it's not like I've come from a pristine background of relationships with officialdom," he said.
"But one thing I will say is that once the game is done and dusted, I'm as good as gold with anyone."
(Editing by Ed Osmond)
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