James O'Connor darted in for the late try that gave the Reds victory over a Brumbies side who had three players sin-binned.
The Brumbies will go in search of back-to-back Super Rugby AU titles when they face the Reds at Suncorp Stadium next weekend.
The Reds forged a comeback at the Suncorp Stadium to continue their perfect start to the Super Rugby Australia season.
A Super Rugby loss came as a significant shock to the Crusaders, but it was a familiar feeling for Waratahs as they fell short again.
Len Ikitau and Andy Muirhead scored twice to set the Brumbies on their way to a 42-14 victory over Western Force on Friday.
The Reds won in remarkable circumstances in Super Rugby AU, while the Super Rugby Aotearoa champions prevailed in much more routine fashion.
The Rebels could not make their man advantage count as Ryan Lonergan's heroics off the bench sealed victory for the Super Rugby AU leaders.
The Brumbies scored 35 unanswered points in the second half to clinch a record win over the beleaguered Waratahs.
Noah Lolesio returned from two months out with a torn hamstring to inspire the Brumbies to glory over the Reds in the Super Rugby AU final.
The ruthless Brumbies scored five tries to see off Western Force and ensure they will be at home in the final on September 19.