The NSW Waratahs have breathed fresh life into their Super Rugby campaign with a crucial comeback win over the conference-leading Melbourne Rebels.

Rocked by the Israel Folau firestorm, the Waratahs overcame a week of turmoil and a 13-point halftime deficit to down the Rebels 23-20 on Saturday night and regain control of their finals fate.

Inspired by skipper Michael Hooper in the champion flanker's 100th game for NSW, the Waratahs' third win from as many starts at the SCG may well have saved their season.

After falling seven competition points adrift of the Rebels after a last-start loss to the Blues, the Tahs are suddenly back in the box seat in the Australian conference.

With the Rebels having a bye next week to stew over successive defeats, the Waratahs can go top of the conference with another home triumph over the Sharks next Saturday night.

The Waratahs' season looked like slipping away after a three-from-seven start and then having Folau, Super Rugby's all-time leading try-scorer, issued with a breach of contract notice by Rugby Australia on Wednesday for his homophobic social media posts.

But after standing down Folau as the Wallabies superstar fights to save his career, the Waratahs stepped up in a steely show of resilience as big guns Hooper, Bernard Foley and Kurtley Beale showed their class.

Replacing Folau at fullback, Beale's kicking game was superb, while Foley enjoyed a unanimous points win over Quade Cooper in their much-anticipated five-eighth duel.

Foley scored all 16 points in the Waratahs' second-half fightback, the match-winning haul coming from a 50-metre try - when he beat Cooper to a loose ball at the back of a lineout - three penalty goals and a conversion.

The Rebels suffered an early blow with winger Jack Maddocks forced out of the game in the second minute after failing a HIA following a head clash with NSW opposite Cam Clark.

When Waratahs veteran Adam Ashley-Cooper strolled over in the 18th minute after a nice inside ball from Jed Holloway, it looked like a long night coming for the visitors.

But tries to Billy Meakes and Reece Hodge plus a long-range penalty goal to Hodge in his milestone 50th Super Rugby game earned the Rebels a 20-7 halftime advantage.

It was all the Waratahs after the break, though, as the Rebels paid the price for conceding eight straight penalties in the second half, allowing Foley to take the game by the scruff of the neck.

"That bloke has so much ticker," Hooper said of Foley.

"He rises to the challenge when he gets put under the pump.

"He had a great game and led us so well."

Victory also allowed the Waratahs to retain the Weary Dunlop Shield.

Foley felt the Folau controversy galvanised the Waratahs.

"We had a bit of a different week but the guys really came together," he said.

"To come out tonight and get the result shows what we have as a team."