At 31-17 up in the 62nd minute, Will Harrison had the chance to clear his line after the Waratahs won a much needed penalty.
He failed to find touch with his left boot and one phase later the Rebels, albeit dubiously because of an obstruction that was missed on the field, Marika Koroibete scored just inside the field of play.
It was the turning point in the second half and the moment looks likely to kill off the Waratahs' finals aspirations.
Eight minutes later the Rebels were in again as Isi Naisarani powered over to cut the score to two points.
Harrison responded, he pounced on Michael Hooper's charge down and swan-dived under the sticks in the 73rd minute and his conversion extended the margin out beyond a losing bonus-point for the Rebels.
But Matt To'omua's late penalty brought the Rebels inside the required seven points and they snatched a crucial bonus-point despite going down 38-32 in a cracking contest at Leichhardt Oval.
✨ Some Marika magic! #SuperRugbyAU #REBvWAR.
— RUGBYcomau (@rugbycomau) August 29, 2020
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When reflecting on the game, Waratahs coach Rob Penney said it "felt a bit like a loss".
The experienced New Zealand coach then pin-pointed two moments in the second half that were crucial in the Rebels' comeback, beginning with Harrison's failure to find touch.
"Two critical moments, I guess, that we had control over," he said.
"We had a penalty over on the far side and Harro unfortunately missed touch and on the back of that, Joey Walton, clearly smashed out of the 'd' line (by Billy Meakes) and they scored on the back of that.
"Then there was a moment in the midfield there where we turned the ball over. Jake (Gordon) had a wee probe down the side and the ball went free, so they're moments in the last 10 minutes that we had an opportunity to control and just a couple of little errors (hurt us)."
By winning the Waratahs (19) moved four points clear of the Rebels on the standings, but the Rebels can leapfrog them into third spot if they beat the Western Force by four points or more next Saturday in Newcastle in the final round of the regular season.
The Waratahs have the bye-round to finish the regular season.
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