The brothers, who say they are innocent, are accused of having formed an organised criminal network in early 2021 in Romania, as well as in the US and Britain
The Rebels snapped a six-game losing streak against the 'Tahs earlier this year and a masterclass from Wallaby fly-half Toomua was again at the heart of their performance.
He booted five penalties and two conversions while directing operations from midfield as his side scored two tries to Waratahs' one.
It handed them a maiden victory in Super Rugby AU, after a draw and a loss.
"A bit of a reward, we had a really good week's prep and it paid off," said Rebels captain Dane Haylett-Petty.
"From the very first minute we felt like we controlled the game and we were able to close it out this time, turn pressure into points at the end."
The Waratahs have managed only one victory from four in the domestic competition, with ill-discipline costly them dearly, conceding 17 penalties on Friday.
Alex Newsome, the stand-in skipper after Rob Simmons went off injured, admitted they gave away too much possession and paid the price for twice being reduced to 14 men.
"I think (ill-discipline) has been a bit of an issue for us this whole competition and it snuck in again today," he said.
"Too many rolling away penalties and offsides and it's really hurting us. But full credit to the Rebels, they had 70 percent possession and 70 percent territory. They got the jump on us physically tonight as well."
The Rebels started strongly and had a try disallowed for a knock-on after just three minutes, before the trusty boot of Toomua put them in front.
The advantage didn't last long after Reece Hodge lobbed a careless pass which Newsome intercepted, sprinting to the line, with Will Harrison converting.
But poor discipline started creeping into the Waratahs' game and they gave away two penalities in quick succession which Toomua expertly put through the posts, before Harrison pulled back three points after some aggressive attacking play.
The Waratahs were straying offside too often and the referee finally had enough, yellow carding Wallabies captain Michael Hooper.
It proved costly with the Rebels bagging 10 points while he was in the sin bin, including a try for Ryan Louwrens to give them a 19-10 half-time lead.
The second period proved tighter, with the Rebels dominating possession and creating chances with some hard running without being able to breach the 'Tahs defence.
But the home team eventually ran out of steam when Jed Holloway became their second player yellow carded and Marika Koroibete clinched the game with three minutes left after finally punching through their defensive line for a well-earned try.
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The brothers, who say they are innocent, are accused of having formed an organised criminal network in early 2021 in Romania, as well as in the US and Britain
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