Australia were given a scare when star flyhalf Quade Cooper was suddenly added to the 'doubtful' list ahead of their opening Tri-Nations match against South Africa in Sydney on Saturday.

The Wallabies remain optimistic that Cooper will recover from illness in time to tackle the Springboks.

However, Cooper sat out Friday's captain's run as he battled flu and gastro.

The Wallabies team doctor doesn't believe his condition is serious enough to prevent the playmaker from lining up for his first Test of the year, although the debilitating after-effects may be a cause for concern.

Despite the untimely disruption to Australia's final training session before the big match, skipper Rocky Elsom said the Wallabies made the right call keeping their trump card rugged up inside while the relentless rain continued to bucket down in Sydney.

"If he's not feeling that well, it's best that he just gets better and feels better tomorrow," Elsom told a media scrum in Sydney.

"It was probably a good move not to train, but I think he'll be fine tomorrow [Saturday]."

Elsom was so confident Cooper - who later joined his teammates at lunch - would be on deck that he said a possible replacement in the Australian backline had not even been discussed.

In Cooper's absence from Friday's session, fullback Kurtley Beale and wing James O'Connor both ran at flyhalf with no other player joining the backline.

"It was alright. You've got to be able to deal with that," Elsom said.