To make matters worse for Waratahs coach Michael Cheika he also saw skipper Dave Dennis limp out of the game in the second half with a leg injury. Despite winning five of their previous six games, successive defeats to the Melbourne Rebels and now the Crusaders have seen Cheika's side drop to eighth in the rankings.
"It's my dressing room that is shattered because they played their hearts out. They deserved to win," Cheika told The Age.
It means their chances of reaching the play-offs are in the hands of other teams with only two Super Rugby games left, against the Western Force and Queensland Reds.
Meanwhile, the Brumbies maintained their fight for first place with a 30-23 home win over the Hurricanes that keeps them on top of the Australian Conference. The Queensland Reds meet the Melbourne Rebels later this weekend to try to stay in touch.