Khawaja, Green hundreds propel Australia to 480 v India
Khawaja and Green were the bedrock of Australia's innings with a 208-run stand for the fifth wicket, the highest partnership from either side in the bowler-dominated series.
Khawaja's batting masterpiece was spread over 10 hours during which the opener faced 422 balls, the most by an Australian batter in India, hitting 21 fours.
India, who lead the series 2-1, were 36 for no loss in reply with Rohit Sharma (17) and Shubman Gill (18) seeing off the final 10 overs of the day.
The home side trail by 444 runs in the match, which they need to win to seal their place in the final of the World Test Championship against Australia in June.
Earlier, on a flat track where the ball did not really turn and reverse swing did not materialise, Khawaja and Green, who made a fluent 114, piled on the runs in the morning session.
Green showed his growing confidence by hitting Umesh Yadav for three boundaries in an over and brought up his hundred with a four off Ravindra Jadeja.
The beaming all-rounder took off his helmet and soaked in the applause before being hugged by Khawaja.
"You never know when that's going to happen, incredibly grateful for it," Green said of his maiden test hundred.
"To be out there with Uzzie for my whole innings, it helped me so much out there.
"Obviously he's got an experienced head, has played beautifully this whole series," Green said of his "special" partnership with Khawaja.
Ashwin (6-91) finally broke the stand when Green attempted a sweep shot and managed to glove the ball to wicketkeeper KS Bharat.
Ashwin removed Alex Carey in the same over and Khawaja fell to the first ball after the tea break when Axar Patel trapped him lbw.
The batsman was initially adjudged not out but India reviewed the decision which was overturned after replays confirmed the ball would have gone on to hit the stumps.
Todd Murphy (41) and Nathan Lyon (34) chipped in with useful cameos before Ashwin wrecked their lower order.
"We expected this wicket to play well, but not as slow as it did," Ashwin told reporters.
"Let's hope this gets tougher to bat on as the game goes on."
Australia players wore black armbands to honour skipper Pat Cummins' mother Maria who passed away overnight.
Steve Smith continued to lead Australia in the absence of Cummins, who flew home to be with his mother after the second test in Delhi.