Although India struggled in their chase of 314, Kohli hit his 66th overall ton in style and at a point when the team needed the most.
He now has the most hundreds in India-Australia ODIs in India. The record was previously held by Sachin Tendulkar. It was also Kohli's 25th ton while chasing and so far, India have won on 21 occasions.
Kohli came in to bat early as Shikhar Dhawan was dismissed by a fantastic catch by Glenn Maxwell. Rohit Sharma followed Dhawan in the very next over and Ambati Rayudu two overs later as India were left reeling at 27/3 from 6.2 overs.
Kohli was joined by Mahendra Singh Dhoni in the middle and the duo put on a 59-run stand for the fourth wicket and recovered the innings to some extent before the Ranchi boy fell for 26 off Adam Zampa.
The 30-year-old reached his fifty off 52 balls in the 24th over.
This was the second century of the series for him and 8th against Australia in ODIs and 15th overall across all the formats against them.
It was also Kohli's 25th ton while chasing and so far, India have won on 21 occasions.