The Crusaders fell short in their bid to reach the Trans-Tasman showpiece match, which will be contested by the Blues and Highlanders.
The Chiefs claimed four points to remain within reach of the top two ahead of the final round of Super Rugby Trans-Tasman fixtures.
The Hurricanes and the Highlanders each made it two wins from two games in Super Rugby Trans-Tasman.
Tense finishes went in the favour of the Crusaders and the Chiefs in Super Rugby Trans-Tasman, while the Blues were emphatic victors.
Saturday's defeat left the Waratahs with a 0-8 record in Super Rugby AU this season.
The Rebels have lost the versatile Reece Hodge for the remainder of the season after he was injured in a loss to the Western Force.
The Rebels failed to turn dominance into points and were shocked as a late try secured victory for the Western Force on Friday.
After suffering back-to-back defeats, the Blues responded with a much-needed win over the Hurricanes in Auckland.
The Waratahs left their rally far too late in a fourth straight defeat on Friday, losing to a Rebels team inspired by Matt Toomua.
Western Force pushed hard for a late comeback but the 14-man Rebels survived to record an important victory.