Needing a win in the final match of the regular season to claim a wild card, the Waratahs got tries from Lachie Turner, Sitaleki Timani, Chris Alcock, Sosene Anesi and Dave Dennis with Kurtley Beale adding 16 points from his boot.
The Waratahs will travel to New Zealand or South Africa for their first-round encounter next weekend while the Bulls and Sharks will battle it out later on Saturday for the final spot in the six-team playoffs.
Wallabies fullback Beale was again impressive, setting up the first try for Turner and kicking well, but the Waratahs have built their season on rock-solid defense.
"The guys worked hard tonight, particularly in the forward, and won that contest up front which opened it up a bit for the backs," Waratahs captain Phil Waugh said in a televised pitchside interview.
"It doesn't bother us where we play, we've worked hard to get where we are and now it's just a matter of getting up there and performing next week." Brumbies flyhalf Matt Giteau finally managed to breach the Waratahs defense after the final siren had sounded to set up a consolation try for replacement winger Francis Fainifo.
The Waratahs could have scored three tries in the first 10 minutes but in the end had to be satisfied with Turner's score, the winger outpacing the cover defense after Beale ran through winger Andrew Smith and released him at halfway.
In the event, they had to wait another 43 minutes for the second, which came when lock Timani drove over from close range early in the second half.
Replacement flanker Alcock showed the benefits of straight running in the 60th minute by crashing through four tackles to extend the lead to 27-0.
Winger Anesi grabbed the fourth nine minutes later when he won a foot race to Luke Burgess's hack through and kicked the ball on to touch down under the posts.
Number eight Dennis got a reward for a fine performance by rounding out the Waratahs' try count four minutes from time with an unspectacular dive over the line.
The twice-champion Brumbies had won their last two matches but failed to finish what has been an otherwise miserable season on a high.
"We were just outplayed, credit to the Waratahs," said Giteau, who will leave for France after the World Cup.
"Their defense was really good and at the breakdown they really dominated us."
