It was initially feared that Barnes had broken his wrist but Waratahs head coach Michael Cheika suggested it was a dislocated and broken thumb.
"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."
Regardless of the nature of injury it is bad news for Robbie Deans, who has already lost David Pocock for the Lions tour.
Barnes was making his first start of the 2013 Super Rugby campaign following a knee injury. But he lasted just 17 minutes before falling his wrist.
He now faces a race against time to impress Deans ahead of the arrival of Warren Gatland's Lions Down Under in June.
The Wallabies fly-half and centre jerseys are still up for grabs and Barnes was a front-runner for Test selection.
The loss to the Cheetahs was the Waratahs' third in four games and their 11th defeat in 12 matches and Cheika admits his side are up against it.
"We are obviously going to be heavily criticised and, first and most importantly, we've put ourselves in a difficult position on the table," said Cheika.
"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."