Bernard Foley was good with the boot for the Waratahs. Photo: Kiyoshi OTA/EPA

SYDNEY  Waratahs rallied from behind on Saturday to win their first match since Israel Folau was stood down over anti-gay comments, as the Highlanders snapped a five-match losing streak to beat the Blues.

The deeply religious Folau, Super Rugby's all-time leading try scorer, is facing the sack over his controversial social media posts, with an upcoming tribunal to decide his fate.

It was a major distraction for his team in the lead up to their clash in Sydney with the Melbourne Rebels, but they put it aside to snatch a 23-20 victory, with Bernard Foley scoring a try and kicking five goals.

"We just wanted to get out on the field and play tonight. I couldn't be happier," said Waratahs skipper Michael Hooper, who made his 100th appearance for the side.

"Some ill discipline gave them a leg up in the first half, but we knew if we stuck to our game plan and sharpened up our penalties we would have a good shot."

In Folau's absence, Kurtley Beale moved into his fullback position and took several high balls with ease, with Karmichael Hunt and Adam Ashley-Cooper in the centres.

Quade Cooper put the Rebels in front with a penalty before Ashley-Cooper got the first five-pointer, breaking through the defence for his first Super Rugby try since 2015.

Billy Meakes grabbed his fourth try of the season for the Rebels to put them back in the lead and they extended their advantage just before the break with Reece Hodge finding a gap in the defence to dot down. 

Hodge then booted a penalty to send them into half-time with a 20-7 lead.

But two Foley penalties pulled the Tahs back to within seven points in the second stanza and he then picked up a lineout overthrow to sprint from almost in his own half for a touchdown.

He converted his own try to draw them level at 20-20 and another penalty gave them the lead and ultimately the win to move them within three points of the Rebels at the top of the Australian conference.

In Dunedin, an acrobatic Shannon Frizell sparked a Highlanders revival as they rallied to beat the Blues 24-12. 

It was all Blues for most of the first half before Frizell put the Highlanders on the board by diving over a ruck to score. From there they took control to lift themselves off the bottom of the New Zealand conference.

The Blues remain in third place, behind the Canterbury Crusaders and Wellington Hurricanes, but have not won an away match in New Zealand since round two of the 2013 season.

"Our defence did a good job because they’ve got x-factor right across their team and we managed to work hard for each other and shut that down," said Highlanders' skipper Ben Smith who described the win as "awesome".

Pre-match interest had focused on rival fly-halves Josh Ioane and Otere Black now Damian McKenzie is out of World Cup reckoning.

But neither provided any obvious answers for the All Blacks selectors, although Ioane had a 100 percent kicking record with three out of three.

Veteran Blues centre Ma'a Nonu blasted through the Highlanders' defence to put Tom Robinson over for the opening try in the 22nd minute.

But fortunes were reversed in the run up to half-time when momentum shifted to the Highlanders who were rewarded with Frizell's dive over a ruck to score. Ioane's conversion put them two points ahead.

Their domination continued in the second half and their scrum was able to bully the Blues all-All Black front row to earn a penalty try.

Matt Faddes extended the lead to 21-5 with a runaway try from an intercept on half-way and Ioane added more points with a penalty before the Blues got a consolation try.