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.
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 Reds trailed for most of Friday's clash with the Rebels, but Alex Mafi's two tries helped them pinch victory at the death.
The Brumbies will host the Reds in the Super Rugby AU final next weekend after Brad Thorn's team overcame the Rebels on Saturday.
Cabous Eloff's late try helped the Rebels edge the Force and reach the Super Rugby AU finals.