Will Jordan scored a double and Codie Taylor got another as the Crusaders confirmed top spot and a home final.
Just one point separated the sides in Hamilton, with Damian McKenzie's late penalty sending the Chiefs into second place.
David Havili's drop goal earned the Crusaders a dramatic golden-point victory over the Hurricanes on Sunday.
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.
The Blues' barren run against the Crusaders continued on Sunday as Richie Mo'unga took centre stage.
The Reds won in remarkable circumstances in Super Rugby AU, while the Super Rugby Aotearoa champions prevailed in much more routine fashion.
Codie Taylor scored twice as 2019 Super Rugby champions the Crusaders defeated the Hurricanes 33-16.
Hooker Codie Taylor scored the opening try of the 2021 season as holders Crusaders came out on top in Dunedin.
The Blues and the Crusaders' respective Super Rugby Aotearoa seasons are over after their match on Sunday was called off.
Trailing at half-time, the Crusaders overcame the Highlanders to dodge a make-or-break date with the Blues in Super Rugby Aotearoa.