The Brumbies scored 35 unanswered points in the second half to clinch a record win over the beleaguered Waratahs.
Israel Folau was sacked by Rugby Australia last year, leading to threats towards ex-chief executive Raelene Castle.
The Rebels are on the verge of securing a place in the Super Rugby AU finals despite a 38-32 defeat to the Waratahs on Saturday.
The Waratahs secured back-to-back Super Rugby wins for the first time in almost a year and a half on the Gold Coast.
The Waratahs scored 38 points without reply in the first half as they cut loose in the rain to thrash the Reds in Sydney.
Rob Simmons is on his way out of the Waratahs after agreeing a deal with ambitious Premiership club London Irish.
The Waratahs have been struggling to find form and a resounding defeat to the Rebels also came with an injury setback for their captain.
The Brumbies made it two wins from two in Super Rugby AU as a late try from Issak Fines saw them beat the Waratahs.
The Reds made it two Super Rugby AU wins out of three, but they were pushed all the way by the Western Force.
Western Force made a flying start in their first Super Rugby AU game, but the Waratahs fought back to secure the victory in Sydney.