Bernard Foley's penalty handed Australia a 35-34 victory, with Joubert running straight off the pitch and into a storm of controversy after he earlier yellow carded Scotland's Kiwi wing Sean Maitland for an intentional knock-on on the advice of his TMO Ben Skeen.
World Rugby later put out a statement saying the South African had made a mistake on the Phipps incident, but Hansen said the organisation was part of the problem.
"I've always said it's a really tough game to referee at the moment and we've got to find ways of making it simpler for them to get it right," he said.
"I don't think it's Craig's problem. I think it's the system's fault. You've got technology that sits there and everyone's saying, 'why didn't he use it?'.
Well, he couldn't use it and that's the problem and World Rugby has to fix that problem.
"If he could have used that, then we could have got a different decision, end of story, because referees have made mistakes from the time the game was first refereed ... you've just got to accept that.
"As long as they take breath, they will make mistakes because players do and coaches do. So if you can accept that the best way to avoid that mistake being the game-winning mistake, for want of a better term, is to make sure you're in front by enough for it not to be.
"Quite often when a mistake is made, and it's right at the end of the game, it's obvious for people to see and everyone gets carried away with it. But sometimes they make mistakes at the beginning of the game which make a massive difference to the result, but no one sees those because they're not caught in the emotion of that last-second penalty goal or whatever."
Adding to the intrigue over Joubert is that he hasn't been sighted since.
Former Scotland fullback Gavin Hastings, who described Joubert's penalty and sprint from the field a "despicable act", said the South African should be punished and sent straight home.
Joubert isn't involved in the semifinals and won't play a part in next weekend's final.
