Brumbies flyhalf Christian Lealiifano slotted 13 points from three penalties and conversions of tries by winger George Speight and centre Andrew Smith either side of halftime.
The Brumbies moved to 35 points on the table, nine ahead of the Waratahs (26), who are now ninth overall and in danger of missing out on the top six playoffs.
Each of the three conference winners advance automatically with the three teams with the next best overall records also qualifying.
"We spoke about getting our spacing right and being really aggressive off the line and we did that well in patches," said Brumbies captain Ben Mowen. "But to keep them tryless, I thought the scrambling (defence) was the best thing."
The match proved a tight struggle characterised by bone-shaking collisions in the tackle, with Waratahs hooker Tatafu Polota-Nau twice lying prone on the ground after heavy knocks. The second forced him off before halftime.
Such was the atttritional nature of the match that when the halftime hooter sounded, the only points had come from two penalties apiece to Lealiifano and Waratahs' scrumhalf Brendan McKibbin.
The Brumbies, however, who had made more effective use of their possession kept the ball alive after the hooter had sounded and Speight crossed after 11 phases to give them a 13-6 lead at the break after Lealiifano converted.
The Brumbies again took advantage of the Waratahs' lapse in concentration shortly after the break when Smith crashed over and with Lealiifano's conversion the home side took a 20-6 lead.
The home side's defence also kept the Waratahs inside their own half and forced errors from the visitors who played far too deep, were easily stopped before the advantage line and had little punch to their attack out wide.
Lealiifano added a late penalty for the Brumbies to increase the
scoreline, though he appeared to suffer a bad injury in the final play
of the match with his right ankle caught under a falling player.