The 31-year-old Williamson also sat out the two-Test home series against Bangladesh last month due to the niggling elbow issue.
Jacob Duffy, Blair Tickner, Rachin Ravindra and Hamish Rutherford were released from the initial 20 player squad.
Williamson's elbow injury kept him out of a Test match in India in December and home series against South Africa and Bangladesh.
Having added 123 with Priyank Panchal (47) for the opening stand, India lost Ruturaj Gaikwad (21) in the second over of the third morning, when Rachin Ravindra (2/96) got him stumped by keeper Cam Fletcher.
Mukesh got wickets with the new (4.3 overs), semi-new (35.3 overs) and old ball (57.4 overs)
Three cricketers have been reprimanded for breaching the ICC Code of Conduct during their teams' quarter-finals in the ICC Under-19 Cricket World Cup 2012 in Townsville on Monday.
590 cricketers -- including 370 Indian players and 220 overseas players -- will go under the hammer during the two-day mega auction in Bengaluru on February 12 and 13.
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