Australia struggled in the morning when rookie Indian paceman Bhuvneshwar Kumar struck three times to leave the visitors 4-63 just before lunch.
However, captain Michael Clarke and Matthew Wade did well to steady the ship and combine for a 145-run partnership, but Australia then lost 5-28 to fall to 9-237 before Clarke decided to declare and bowl three overs at India before stumps.
India survived those with Virender Sehwag on four and Murali Vijay yet to score. At stumps, India is 0-5 in reply to Australia 9(dec)-237 highlighted by 91 from Clarke and 62 from Wade, but they got precious little help.
Bhuvneshwar Kumar claimed 3-53 for India with Ravindra Jadeja taking 3-33, Harbhajan Singh 2-52 and Ravi Ashwin 1-41.
Clarke won the toss and elected to bat first on a Hyderabad pitch that did look to have a little more life in it than the dustbowl in Chennai.
India cruised to a big win in that First Test against Australia, but it was with no help from seamers Kumar or Ishant Sharma.
That changed on the first morning of the Second Test with Kumar dismissing David Warner (six), Ed Cowan (four) and Shane Watson (23).
Australia was then 4-63 after Hughes was caught behind by MS Dhoni off Ashwin for 19 attempting a cut shot.
After clearly not selecting a team that was capable of pushing for a win in Chennai, the Australian selectors surprisingly dropped Nathan Lyon for the Second Test in favour of Xavier Doherty with Glenn Maxwell also coming in for Mitchell Starc.
Clarke would have been hoping for a good start from his top-order when electing to bat first, but it wasn’t to be with both Kumar and Sharma finding some life in the Hyderabad wicket.
Warner was the first wicket to fall in the third over when he was bowled by Kumar for just six from eight balls.
Australia was then in trouble at 2-15 when Cowan was trapped in front for four off Kumar as well.
Watson then was beginning to look good on his way to 19 with four boundaries before he attempted a pull shot to a ball that wasn’t that short and that was never going to bounce enough on the low Indian deck.
The ball struck his back thigh and was just in line with the off-stump and clearly going on to hit middle and leg. He was out for 23 and Australia was 3-57 before Ashwin then got rid of Hughes for 19 at 4-63.
Clarke and Wade did well, though, to bat right throughout the day's middle session and then beyond to take the score to 4-208 before Wade fell for 62 to the bowling of Harbhajan.
That sparked a dramatic collapse with Moises Henriques following for five, Maxwell for 13, Peter Siddle for a duck and then finally Clarke for 91 when he was bowled by Jadeja. Clarke then declared just two overs later with three overs in the day left.