The 25-year-old aimed a mighty swipe in the 56th over and was caught at long on by Umesh Yadav off the bowling of Ishant Sharma.
Yadav has been the destroyer for India with his maiden five-wicket haul of 5-93.
Warner had been struck on the ear on 80, dropped at slip on 126 and hit near the elbow on 135 during his 261-minute innings.
A Twenty20 specialist before he secured his baggy green cap, Warner has amassed 383 runs in his five-Test career at an average of 63.83.
Warner's partnership of 214 with Ed Cowan (74) is the highest by an Australian opening pair since Simon Katich and Phil Jaques added 223 against West Indies in Barbados in 2008.
Cowan was bowled by Yadav after adding 34 to his overnight score.
Shaun Marsh was caught at second slip for 11 as the West Australian continued his poor series (14 runs at 3.50).
Veteran Ricky Ponting was bowled between bat and pad by Yadav for seven.
Warner was out after lunch and skipper Michael Clarke (18) fell three overs later, caught behind to Zaheer Khan.
Zaheer, who traded barbs with Brad Haddin this week in the media, dismissed the wicketkeeper/batsman caught behind for a duck at 6-303.
Mike Hussey hit a catch to gully for 14 to hand Vinay Kumar his first Test wicket and Peter Siddle contributed 30.
Mitchell Starc was 15 not out.
Australia lead the four-match series 2-0 and need only to draw the Perth Test to regain the Border-Gavaskar Trophy.
- AAP