Wallabies playmaker Berrick Barnes suffered a dislocated thumb as the NSW Waratahs' Super Rugby woes continued on Friday night.

The Waratahs slumped to a 27-26 loss to their South African bogey side the Cheetahs and Barnes' latest setback only compounded their misery at Allianz Stadium.

Making his first appearance of the season after missing the opening month of the competition with a knee injury, Barnes appeared to get hurt while making a try-saving tackle on giant Cheetahs lock Lodewyk de Jager in the 17th minute.

Dejected coach Michael Cheika was unsure how serious Barnes' injury was.

"It went back in, obviously, so we'll just see," Cheika said.

"We won't know for at least 48 hours. We've got to wait."

NSW's defeat was their second straight and the Tahs also take a dubious place in the Super Rugby history books as the first team to lose three times in a row to the Cheetahs.

"We are obviously going to be heavily criticised and, first and most importantly, we've put ourselves in a difficult position on the table," Cheika said after his side's third defeat in four matches and 11th loss from their past 12 games.

"We're a team who is carrying a lot of anxiety as it is from past seasons.

"So we're going to get a lot more of that now and we have to have the resolve to understand that we're going to be in a massive war - with ourselves predominantly - and we have to have the courage and the application to make the sacrifice to get out of it because no one else is going to think we can."

Adding insult to injury, former Waratahs halfback Sarel Pretorius was the architect behind the South Africans' triumph, putting lively winger Raymond Rule over for the match-winning try 10 minutes from fulltime.

A 40th-minute try to centre Adam Ashley-Cooper had given NSW an unlikely 20-17 lead at the break after the Cheetahs had dominated possession and territory in the first half.

Centre Robert Ebersohn benefited from a lovely chip and regather from winger Willie Le Roux to score the visitors' opening try after just 54 seconds.

The Cheetahs were in again in the 17th minute when Rhule stepped his way over for the first of his two tries and five-eighth Johan Goosen again converted.

Two penalty goals from halfback Brendan McKibbin kept the Waratahs in touch at 14-6 before winger Peter Betham ran a nice line from a lineout win and took a short ball from McKibbin and beat two defenders to score under the posts.

McKibbin's conversion left NSW trailing by a point but, after Goosen added a penalty to nudge the Cheetahs four points ahead, the Waratahs snatched the halftime lead when Ashley-Cooper touched down on the stroke of halftime.

Goosen and McKibbin traded second-half penalty goals before Goosen's conversion of Rule's second five-pointer restored the Cheetahs' advantage.

Another McKibbin penalty in the 73rd minute reduced the deficit to one point but the Waratahs were unable to bridge it.

Apart from Barnes, prop Benn Robinson also failed to see out the match, being bizarrely replaced before the second-half kick-off despite running on after the interval.

Robinson slumped to the ground, seemingly ill, and had to be escorted off.