The Brumbies finished on top in Sydney for their first win at Allianz Stadium since 2002 thanks to a Joe Tomane hat-trick, winning 26-20.
Two quick tries from Tomane suggested this was going to be a one-way contest but the Waratahs showed plenty of heart to fight back through scores by Reece Robinson and Israel Folau.
Tomane's hat-trick try though and the boot of Christian Lealiifano gave the Brumbies enough of a winning margin in the second half to close out their fifth win of the season.
Folau's night at outside centre looked to be over after 30 seconds when he was knocked out in a head clash with Jordan Smiler, but he returned somewhat surprisingly after passing a concussion test.
His partnership in midfield with Kurtley Beale showed flashes of promise, as did young full-back Andrew Kellaway, but despite making most of the running the Waratahs lost out too often in the collisions and set-piece, failing to get past the Brumbies defence in the second half as the breakdown served up a feast of penalties for both sides.
Slick hands and a well-executed kick from Tomane had the Brumbies in position deep in Waratahs' territory, and after a lineout steal the Wallaby winger was on hand to cut inside a hapless Nick Phipps for the game's first try.
Soon after Tomane was at it again, a clever loop from Lealiifano with Stephen Moore creating the overlap before Tomane pinned his ears back down the touchline and beat Kellaway easily with a big sidestep to grab his second try and make it 12-0.
Quick passing helped the Waratahs hit back – Will Skelton's offload releasing the fleet-footed Jed Holloway before the number eight put away Robinson for his first try in Super Rugby.
Skelton's hands showed the Waratahs how to unlock the Brumbies defence and they almost did it again after good work from Kellaway, ending up with a penalty for a high tackle which Foley slotted to make it 12-10.
The Waratahs followed that up with a stunner, Folau matching Lote Tuqiri's try-scoring record for the 'Tahs on 29 as he finished off a sublime attack all started by Beale's inside ball to Kellaway.
On his first start the full-back stepped on the gas before drawing the last man to put Folau away, as the Waratahs completed an impressive turnaround to lead 17-12 after Foley's conversion.
The Brumbies' response was instant, kicking to the corner and scoring off what's fast becoming a trademark rolling maul through captain Stephen Moore.
Lealiifano restored the Brumbies lead with the conversion and they led at half-time 19-17, but only just after Matt Carraro failed to haul in a looping pass faced with a one-on-one against Aidan Toua. With every attack though, the Waratahs looked threatening.
Discipline at the start of the second half threatened to hurt the Brumbies but they escaped without coughing up any more points, a monster scrum getting them out of trouble.
Faced with the option of going for the posts after the Waratahs entered the ruck from the side, instead the Brumbies knocked the penalty into the corner and after another thundering maul they flung it wide for Toua to put Tomane away into the corner for his hat-trick, his second in Super Rugby, making it 26-17.
Moore and his pack were growing in confidence as they opted for a scrum from a penalty close to the Waratahs line, only for referee Nick Briant to hand the scrum to the Waratahs after the Brumbies failed to use it.
Instead it was the Waratahs now applying persistent pressure, trying to hurt the Brumbies through their own rolling maul but ultimately failing to execute.
Composure was vital for the home side if they wanted to turn the result in their favour, except veteran back-row Wycliff Palu saw yellow for charging with the shoulder off his feet into a ruck, leaving the Waratahs down to 14 for the closing stages.
Brumbies flanker Jarrad Butler joined Palu on the sidelines after putting his hands in the ruck, Foley shortly after landing his second penalty to put the Waratahs in losing bonus point range at 26-20.
There was still time for the Waratahs but a late knock-on snuffed out their chances, as the Brumbies at last defeated the Waratahs at this ground for the first time in 14 years.
Tries: Robinson, Folau
Cons: Foley 2
Pens: Foley 2
Yellow Card: Palu
Tries: Tomane 3, Moore
Cons: Lealiifano 3
Yellow Card: Butler
Waratahs: 15 Andrew Kellaway, 14 Reece Robinson, 13 Israel Folau, 12 Kurtley Beale, 11 Matt Carraro, 10 Bernard Foley, 9 Nick Phipps, 8 Jed Holloway, 7 Michael Hooper (c), 6 Jack Dempsey, 5 Will Skelton, 4 Dean Mumm, 3 Tom Robertson, 2 Hugh Roach, 1 Benn Robinson
Replacements: 16 James Hilterbrand, 17 Paddy Ryan, 18 Angus Ta’avao, 19 Sam Lousi, 20 Wycliff Palu, 21 David Dennis, 22 Matt Lucas, 23 David Horwitz
Brumbies: 15 Aidan Toua, 14 Robbie Coleman, 13 Tevita Kuridrani, 12 Matt Toomua, 11 Joe Tomane, 10 Christian Lealiifano, 9 Tomás Cubelli, 8 Jordan Smiler, 7 Jarrad Butler, 6 Scott Fardy, 5 Sam Carter, 4 Rory Arnold, 3 Ben Alexander, 2 Stephen Moore, 1 Scott Sio.
Replacements: 16 Josh Mann-Rea, 17 Allan Alaalatoa, 18 Les Leuluaialii-Makin, 19 Tom Staniforth, 20 Michael Wells, 21 Joe Powell, 22 James Dargaville, 23 Nigel Ah Wong
Referee: Nick Briant
Assistant Referees: Brendon Pickerill, Michael Hogan
TMO: Ian Smith