Scans on Friday confirmed the hulking lock had sustained a "minor" calf strain and Richie Arnold trained in his place at Stade Geoffroy-Guichard with hooker Dave Porecki leading the captain's run.
"We're giving Will as much time as possible to get ready for the game so he's in treatment, he's working with the physios at the moment," assistant coach Dan Palmer told reporters.
"We'll give him until the last minute to be ready. There's no mind games... he's an important part of our team and we're prepared to do that."
Palmer confirmed that Porecki would lead the team if Skelton was not available, while Matt Philip would move onto the bench as replacement lock.
"Dave, given the opportunity, he'll be superb," said veteran prop James Slipper.
"The way he goes about his business on the field as a player, he leads by example.
"He's just one of those players who's really measured, really calm, composed, really world-class in his craft and he's got the respect of the boys."
Skelton's injury is a second blow for Australia this week as they prepare for a match which could all but earn them a place in the quarter-finals.
Tighthead prop Taniela Tupou will miss the match after sustaining a hamstring strain also described as "minor" by team officials.
That means 34-year-old Slipper, who missed the last two matches with a foot injury, will swap sides of the front row from loosehead as he becomes the third Australian to play in four World Cups.
"There was a point a couple of weeks ago where I probably thought it might not happen," he said. "But lucky enough to get through that injury and lace up this weekend.
"It will be without (Taniela) at tighthead, which would be a preference of mine, but I'm excited to be out there putting on the jersey again."
Slipper, a member of the Wallabies side that reached the 2015 World Cup final, will play his 132nd test on Sunday and further close the gap on George Gregan (139) as the most capped Australian.
"I didn't come over here to break records," said Slipper. "I really wanted to come here and win the World Cup."
