Hughes failed again, falling for a duck to first Test destroyer Ravi Ashwin, as Australia were two for 74 at stumps chasing down the hosts’ total of 503 at Rajiv Gandhi Stadium.
The Macksville lad who rebuilt his technique and was scoring freely in domestic cricket before his recall could be dropped for the third time in his career having posted scores of 6, 0, 19 and 0 so far in the four-Test series.
Ashwin bowled both David Warner (26), who looked dangerous, and Hughes (0) around their legs.
Opener Ed Cowan (26) and Shane Watson (9) were not out at stumps and will face an uphill battle to take the match to a fifth day.
Australia came in to bat after Xavier Doherty (3-131) and Glenn Maxwell (4-121) wrapped up the Indian lower order having been giving a pasting earlier by Murali Vijay (167) and Cheteshwar Pujara (204).
The best thing to happen for Oz happened in the crowd, with Test legend Merv Hughes taking a ripper of a catch in the crowd from a Warner six.
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VIDEO: Merv Hughes takes catch in crowd off a Warner six (4/3)