James O'Connor darted in for the late try that gave the Reds victory over a Brumbies side who had three players sin-binned.
Richie Mo'unga won his kicking battle with Damian McKenzie as the Crusaders triumphed in the Super Rugby Aotearoa title match.
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 Chiefs were much-changed for their Super Rugby Aotearoa match against the Blues, who still had to work hard for a 39-19 victory.
It was a Super Rugby Aotearoa season with few highs for the Hurricanes, but they finished with a flourish against the Highlanders on Friday.
Will Jordan scored a double and Codie Taylor got another as the Crusaders confirmed top spot and a home final.
Saturday's defeat left the Waratahs with a 0-8 record in Super Rugby AU this season.
The Hurricanes appeared set to clinch just their second win of the season, only to be beaten by a last-gasp penalty on Friday.
A thrilling contest between Western Force and Waratahs was settled in the hosts' favour when Domingo Miotti struck late on.
Just one point separated the sides in Hamilton, with Damian McKenzie's late penalty sending the Chiefs into second place.