Sri Lanka's 2019 World Cup participation is now uncertain as they failed to get the number of victories required for automatic qualification.
Kohli said the good show in Sri Lanka will boost the confidence of his side when they take on Australia in a five- match ODI series starting later in September.
Dhoni became the first to achieve the feat, surpassing former Sri Lankan wicketkeeper Kumar Sangakkara who had 99 stumpings to his credit. His leading edge went straight into the gloves of India wicket-keeper Mahendra Singh Dhoni, and the Sri Lanka skipper fell short of his half-century. Instead it was Ajinkya Rahane (No. 27) opening with Rohit Sharma (No. 45).
Akila Dananjaya's six-wicket tow in the second game crucial, so it is simply India received a sumptuous feast of a series.
Another reason to get to this milestone has been the support of the spinners as India have often played two spinners both home and away.More news: Greenstone | Plants and friends - gorgeous weeds and how to grow them - wunderbare Unkräuter und wo sie zu finden sind
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Sri Lanka appeared to be heading towards another low score when Lahiru Thirimanne and Angelo Mathews joined hands with the hosts at 63/3.
Kohli smashed nine boundaries in his 116 balls knock.
Sri Lanka squandered the opportunity to salvage some pride, folding up for a below-par 238 in 49.4 overs after paceman Bhuvneshwar Kumar grabbed a career-best 5-42. The left-handed batsman played on to an in-swinging delivery while attempting a cut to third-man. This is also his maiden five-wicket haul in the 50-over format.
At one stage of the game it looked like the hosts would post a total well in excess of 280 when they were cruising at 185-3 in the 39th over. We lost a few early wickets.