The incident came in the wake of a record 64-7 drubbing for the Rebels in their match against South Africa's Sharks in Durban on Saturday and both players were stood down after an club investigation on Sunday.
"The club will not tolerate this type of behaviour and I am embarrassed for everyone associated with building this club," Rebels coach Damian Hill said in a team statement.
Rebels chief executive Steven Boland said the ARU had been consulted as both Beale and Vuna are also centrally contracted by the Wallabies.
"There can be no excuses for the disrespect shown to the Melbourne Rebels Rugby Club by these players," he said.
"The expectation of the club and our supporters is that the management and players in South Africa focus immediately on their task of making amends for the poor on field performance in Durban on Saturday by making us all proud in Bloemfontein next weekend."
Both players are almost certain to miss the match against the Cheetahs next weekend.
Beale, who will be a strong contender for the Wallabies flyhalf role for the three tests against the British and Irish Lions in June and July, is till under a legal cloud after being charged with assault after a fracas at a nightclub last year.
Rugby league convert Vuna made two appearances on the wing for the injury-ravaged Wallabies last year but would be a fringe player at best for the Lions series.