Lee is unlikely to be fit for the next Test after scans showed he is on the verge of suffering a stress fracture on his left foot.
Lee, who faces four to six weeks on the sidelines, did not take the field on the third day at the MCG as Australia's inexperienced attack was plundered by the Proteas' tail. But he may still bowl again in the ongoing match.
Scans last night showed the 32-year-old fast bowler was suffering a stress reaction in the fourth metatarsal bone, but x-rays today revealed no break.
The injury is another setback to Lee - who has series figures of one for 200 against South Africa and has taken only 21 wickets at 45.5 since the start of Australia's unsuccessful series in India.
Team physio Alex Kountouris reported it is "inevitable" Lee will need rest.
"I don't think he'll be able to play the Sydney Test. We'll wait and reassess at the end of the game," he said.
"If he's got what we think he's got - and it's been confirmed by scans that he's got a stress fracture brewing - we're going to rest him for a period of time to get it to settle."
Short-term future
Lee will, however, be given every chance to bowl in the second innings at the MCG.
"Short-term future is we're going to try and get him to bowl in the second innings," Kountouris added.
"We're doing everything we can to settle it down, have one good go at it in the second innings.
"Keep Lee off cricket for a while"
"He might bowl one ball; he might bowl 10 overs or 15 overs."
Kountouris admits there is a risk Lee, who will not be given painkillers to see out the match, could end up breaking the bone should he bowl in the second innings.
"But in some people's opinion that might be a better scenario, because the bone heals better," he said.
"Tiny crack"
"If you have a tiny crack it can take a long time for it to heal. That's not what we're aiming for, but there is a risk of that happening. Pain will guide us to where he is.
"There was so much pain he couldn't bowl today; he wouldn't bowl if he was in the same pain the second innings."
Should Lee not be fit to bowl again in the match, Australia will be left with only three frontline bowlers to dismiss South Africa a second time and level the series.
"I guess we'll have to wait and see whether he can bowl first. But no doubt losing Brett Lee out of your attack will certainly have an effect on your team," said Australia vice-captain Michael Clarke.
