Jadeja suffered a blow to his left thumb and dislocated it when he was batting on the third day of the drawn Test, adding to India's long injury list.
"He later went for scans and the results have shown that he has dislocated his thumb," the BCCI said in a statement.
"The all-rounder will now consult a hand specialist in Sydney before he returns to India. He will then head to the National Cricket Academy in Bengaluru for further management of his injury."
Middle-order batsman Hanuma Vihari is also a doubt after he pulled his hamstring but continued to bat in the middle in order to save the Test for the tourists.
India have already had batsman KL Rahul (sprained wrist), and fast bowlers Umesh Yadav (strained calf) and Mohammed Shami (fractured arm) ruled out of the tour.
The series is tied at 1-1 and the final Test will be held at the Gabba from Jan 15-19, after which India return home for a four-Test series against England that begins on Feb 5.