It was India’s second successive win against the visiting side in the series for the Late Sh. Karan Singh Dalal Memorial Cup.
The third match will be played on Sunday.
Batting first, India scored 192 for seven with opener Yogendra Bhadoria top-scoring with a 49-ball 71.
Skipper Vikrant Keni, who played an unbeaten knock of 53 runs off 40 balls, and Wasim Iqbal with 26 runs in 14 balls, were the other main contributors for India.
In reply, Nepal collapsed for just 39 runs.
Surendra Kumar Khorwal and Akhil Reddy scalped three wickets each, while Vikrant Keni and Ravindra Sante took one apiece.
In the first match, India defeated Nepal by 152 runs.