Bernard Foley has picked the perfect time to score his first try of the Super Rugby season, snatching a crucial 31-26 win for the NSW Waratahs over the Melbourne Rebels at AAMI Park.

The stand-in skipper while Michael Hooper is sidelined with a hamstring injury, Foley gave his team the match-winning lead on Friday night when he intercepted a Billy Meakes pass and raced 50m to touch down.

The Rebels hammered the tryline in the final few minutes and had a lineout after the final siren but the Waratahs' defence held firm to secure the vital win.

Leading the Australian conference over the Rebels by one point before the match, the win gives the Waratahs some breathing space with two rounds to play before the finals.

"It's massive to get the win in terms of the Australian conference," Foley said.

"And also they were exceptionally up for the fight tonight."

The home side will be kicking themselves after leading 26-17 until late in the second half and having all the running.

But an intercept by Kurtley Beale turned over the ball to set up a try for Ned Hanigan in the 69th minute before Foley's intercept try three minutes later.

The Waratahs fightback was all the more gutsy with their preparation was rocked with superstar fullback Israel Folau officially ruled out less than 24 hours before kick-off.

His appeal against a one-match suspension stemming from aerial contact in the last Test against Ireland was dismissed late on Thursday night.

"I'm very proud we hung in the fight in a game that for large parts of it, we were outplayed," coach Daryl Gibson said.

NSW led 17-10 at halftime after they took advantage of a Meakes yellow card for sticking his foot out from the breakdown into Nick Phipps' pass.

Winger Taqele Naiyaravoro scored to level Folau's NSW try-scoring record with his 12th for the season.

The Rebels came out firing in the second half with halfback Michael Ruru burrowing in for a try in the 44th minute.

A penalty kick three minutes later by Reece Hodge gave the home side the lead.

Hodge then kept the scoreboard ticking over through penalties but they couldn't go the distance, with the Waratahs key men Foley and Beale standing up.

Rebels coach Dave Wessels said while they were disappointed not to win, they were mostly pleased with the performance.

"It hurts not to win the game but from a performance perspective, I'm incredibly proud," Wessels said.

"We got close to our best rugby and we were unlucky not to win."