The governing body issued a statement on Monday saying the South African had not made the "appropriate decision".
Cheika, whose side won Sunday's match 35-34, said: "No other referee has had this stuff put out there like that.
"I would have liked my mates to back me up a little more."
Former top referee Jonathan Kaplan, who has mentored Joubert during his career, questioned whether World Rugby should be "criticising one if its own assets".