Along with wicketkeeper-batsman Matthew Wade, Clarke put on a century-plus partnership as Australia reached 187 for four at tea, after being reduced to 63 for four during the first session of play.
If the opening session belonged to India, who sent back four top-order Australian batsmen back to the hut, the post-lunch session undoubtedly belonged to the Aussie pair of Clarke and Wade, who put on 124 runs for the unbroken fifth wicket stand.
The Aussie captain was batting on 68 with the help of eight boundaries and a six while Wade, who was in doubt for the match after fracturing his cheekbone during a freak accident during a training session here, reached 55 with the help of seven boundaries.
The duo had their anxious moments but overall they handled the spin troika of Ravichandran Ashwin, Harbhajan Singh and Ravindra Jadeja with ease.
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While Clarke again used his feet to perfection, Wade decided to play with the spin on most occasions as they logged 104 runs in the second session.
After a luckless first Test, where the Indian spinners got all the 20 Australian wickets, India's new ball bowlers, especially Bhuvneshwar gave a much better account of themselves hitting the right areas.
The Australian top-order played shots during the first session but was often troubled by the deliveries that were keeping low.