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Michael Cheika's side scored five tries to one in their bonus-point victory to take over top spot from the Sharks who had a bye this weekend.
With the top two teams hosting semi-finals on the second week of next month's play-offs, the Waratahs are in pole position heading into their final two regular season games against the Highlanders and the Reds.
It was a commanding performance from the Waratahs, who are bidding for their first Super Rugby title after finishing runners-up in 2005 and 2008.
The 31-point winning margin was not far short of their biggest win over the Brumbies of 34 points set three years ago.
Winger Alofa Alofa scored two tries with others going to Wallabies Benn Robinson, Bernard Foley and Wycliff Palu.
Foley kicked four conversions and a penalty while Kurtley Beale landed a penalty.
The injury-hit Brumbies were restricted to just one try with Jesse Mogg outjumping his celebrated rival fullback Israel Folau to score in the first half, while Christian Lealiifano kicked a penalty goal.
The Waratahs played some cohesive rugby to lead 14-5 at half-time and outscored the Brumbies in the second half 25-3.
It was the first time the Brumbies had conceded a bonus point on the road since 2011.
The Waratahs paid a price for their handsome win with skipper Dave Dennis suffering a suspected anterior cruciate ligament injury just before half-time and is likely to be out for an indefinite period.
Wallaby flanker and skipper Michael Hooper, who took over the captaincy from Dennis, said the Waratahs were looking to take their momentum into the play-offs.
"I was very proud that we went to the 80th minute and keep putting points on right to the last minute," Hooper said.
"It's a feature that's come into our game this season and one we want to stick with if we want to be competitive in the finals.
"We said we wanted to be top two at the start of the year and we're on track for that, so we have two games to go."
Brumbies' skipper Ben Mowen said his team had played some moments of championship rugby.
"We were not consistent enough and the 'Tahs were very good tonight but we played a great opening 30 minutes in some of the best effort we've had all year," Mowen said.
"The 'Tahs were outstanding tonight and all their big guys stood up and performed really well and they'll go on."
Scorers:
Waratahs: 39 - Tries: Benn Robinson, Alofa Alofa (2), Bernard Foley, Wycliff Palu; Conversions: Foley (4); Penalties: Foley, Kurtley Beale
Brumbies: 8 - Try: Jesse Mogg; Penalty: Christian Lealiifano
Teams:
Waratahs:
15 Israel Folau, 14 Alofa Alofa, 13 Adam Ashley-Cooper, 12 Kurtley Beale, 11 Rob Horne, 10 Bernard Foley, 9 Nick Phipps, 8 Wycliff Palu, 7 Michael Hooper, 6 Dave Dennis (captain), 5 Kane Douglas, 4 Jacques Potgieter, 3 Sekope Kepu, 2 Tatafu Polota Nau, 1 Benn Robinson.
Substitutes: 16 Tolu Latu, 17 Jeremy Tilse, 18 Paddy Ryan, 19 Will Skelton, 20 Stephen Hoiles, 21 Brendan McKibbin, 22 Jono Lance, 23 Taqele Naiyaravoro, 24 Cam Crawford
Brumbies:
15 Jesse Mogg, 14 Henry Speight, 13 Tevita Kuridrani, 12 Robbie Coleman, 11 Clyde Rathbone, 10 Christian Lealiifano, 9 Nic White, 8 Ben Mowen, 7 Jarrad Butler, 6 Jordan Smiler, 5 Leon Power, 4 Scott Fardy, 3 Ben Alexander, 2 Ruaidhri Murphy, 1 Scott Sio
Subsitutes:16 Luke Holmes, 17 Ruan Smith, 18 Jean-Pierre Smith, 19 Fontunuupule Auelua, 20 Jack Whetton, 21Michael Dowsett, 21 Rodney Iona, 22 Lionel Cronje
Referee: Steve Walsh (AUS)
