Hughes was out for a duck on Monday - his second scoreless knock in four innings in the series - and he has just 25 runs at an average of 6.25.
The South Australia batsman has been out to spin on all four occasions, three times to offspinner Ravi Ashwin.
Hughes and David Warner (26) were both bowled by Ashwin after attempting sweep shots.
India had resumed on 1-311 and were bowled out for 503 at tea for a first-innings lead of 266.
Debutant offspinner Glenn Maxwell claimed 4-127 and left-arm spinner Doherty removed three tailenders in his 3-131 off 46.1 overs.
"We came in today knowing we were up against it and we needed to put in a better day than yesterday,'' Doherty said.
"Today we took nine for 190 or something like that (9-192), which was a pleasing effort.
But the damage was done yesterday so there's still a lot of work for us to do to get ourselves back into the game.''
Doherty didn't take a wicket until his 43rd over and admitted his late flurry of three scalps was a confidence-booster after returning for his third Test and first since 2010.
Australia dropped offspinner Nathan Lyon for the Hyderabad match.
"Not even thinking about the third Test,'' Doherty said.
"It was pleasing in some ways to find a little bit of form during the spell.
"But the selection and that stuff, we've got a couple of days to worry about here before that.
"But Nathan is obviously a quality bowler and he's shown that over the last 18 months.
"I've got no doubt that he'll play again.''
The 370-run partnership between Murali Vijay (167) and Cheteshwar Pujara (204) is the highest by an Indian pair for the second wicket in Test cricket.
No.5 Virat Kohli made 34 and skipper MS Dhoni clubbed 44 off 43 balls but India's innings fell away with the last six wickets tumbling for 43 runs.
Dhoni's India side lead the four-match series one-nil.
- AAP
