South African fast bowler Anrich Nortje rapped Green on his right index finger and forced him to retire hurt, late on the second day of the Boxing Day Test.
Green was batting at No.6 and had made six, with Australian well in control at 3-363 in their first innings on Tuesday.
Defending Nortje's 144km/h delivery, Green had his finger jammed against the bat handle.
The finger was cut and swollen and Green left the field after several minutes of treatment.
A team spokesman said Green had gone to hospital for scans.
It came a few minutes after David Warner limped from the arena in distress, having suffered cramps on reaching 200.
Left-arm paceman Mitch Starc might also not bowl in the second innings after suffering his own finger injury.
Green is a right-arm bowler, meaning this issue could also put him out of the Australian attack for the rest of the Test.
It comes four days after the 23-year-old attracted $3.15 million in the IPL auction - a record price for an Australian player.
On Monday, Green took his best Test figures of 5-27 as South Africa were rolled for 189 in their first innings.
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