Jones was scathing in his assessment of referee Mark Goddard's performance in the game, telling the media: "We were definitely the strongest scrum in the first half, and we get penalised for collapsing the scrum."
"Work that one out. It is disgraceful. This is not good enough. It's not good enough for rugby. We're saying the scrum is a contest, and so the stronger scrum gets penalised. It just doesn't make sense."
Australian Rugby Union and Sanzar chief executive Gary Flowers indicated that the body believes Jones has shown disregard for a pre-season directive regarding the commenting on referees.
"After studying the comments made and meeting today with the tournament director this morning, the matter's been referred to judicial officer Terry Willis," Flowers said.
"I attended the Reds-Brumbies game and the content of the comments by the coach about the match referee was referred to me shortly after it.
"There was a clear message issued to all teams, coaches and administrators before the start of this [Rebel Sport] Super 14 season that there would be zero tolerance of public criticism of referees and officials.
"Coaches know that there is a process by which they can engage match officials after games.
"Statistics out today actually reveal that there are fewer average penalties, scrum resets and free kicks per game in this year's Super 14 competition than in the previous two years, so complaints that referees are penalising teams out of the game don't stand up.
Jones will learn of his ultimate fate regarding the incident at a hearing with the Sanzar judicial officer in the next two days in Brisbane.