Kohli needed just one run to reach the milestone and the batting ace took a single off Lakshan Sandakan to get there. He became the sixth international skipper to reach the mark and the second Indian after Mahendra Singh Dhoni.
Kohli is followed by Ricky Ponting, Graeme Smith, Dhoni, Allan Border and Stephen Fleming.
India beat Sri Lanka by 78 runs in the third and final T20 International to win the three-match series 2-0.
Sent into bat, India rode on K L Rahul (54 off 36) and Shikhar Dhawan’s (52 off 36) 97-run opening stand to post a challenging 201 for six in their allotted 20 overs.
Manish Pandey then smashed 31 off 18 balls and skipper Virat Kohli, batting at number six, scored a brisk 17-ball 26.
Defending the total, the Indian bowlers, led by right-arm pacer Navdeep Saini (3/28) Shardul Thakur (2/19), dished out a disciplined effort to bundle out Sri Lanka for 123 in 15.5 overs.
Off-spinner Washington Sundar also picked up two wickets giving away 37 runs from his four overs.