Despite outscoring the Rebels by three tries to one, the match was in the balance right until the death when the Waratahs were glad to settle for an 18-16 margin of victory.
The home side at Allianz Stadium in Sydney would have had a more comfortable end to the game, had Bernard Foley not missed all three of his conversion attempts, following tries from Michael Hooper, Adam Ashley-Cooper and Rob Horne.
Jack Debreczeni was far more clinical with the boot for the Rebels, slotting three penalties and adding the extras to Bryce Hegarty's second-half try.
Hooper made the breakthrough after five minutes when in a rolling maul he clutched on and allowed team-mates to drive him over the line. Foley's missed conversion would become a bad habit, although he kicked a penalty three minutes later to stretch the hosts' lead to 8-0.
When Ashley-Cooper crossed for a second Waratahs try in the 19th minute, fed by Hooper, it looked set to be a tough night for the Rebels. The television match official rejected suspected obstruction in the build-up to the score.
The visitors from Melbourne had Sefanaia Naivalu yellow-carded before the half-hour mark, while Foley booted a penalty off target.
The Rebels finally put points on the board when Debreczeni booted a penalty a minute before the half-time interval, and they were rapidly closing in on the home side when he added two further successful kicks early in the second half.
Matches between these sides in Sydney are typically won - and won well - by the Waratahs, who had triumphed in all four of their previous home contests against the Rebels.
When Horne grounded the ball for their third try, the pressure looked to be easing.
He darted over in the right corner despite the attentions of three would-be Rebels tacklers. It was not immediately clear if he had legitimately grounded the ball before being barged off the pitch, but the television match official found in his favour.
Another conversion went astray, and the Rebels closed up to just two points adrift when Debreczeni made a burst that led to Hegarty being passed the ball to cross in the corner for a soon-to-be converted try.
Fortunately for the Waratahs, their visitors got no closer. Amid fears over conceding a late penalty to the keen boot of Debreczeni, the game was over when the Waratahs forced a Rebels knock-on.