Angelo Mathews' unbeaten 97 helped Sri Lanka reach a challenging total of 299/8, however, Dananjaya's six-for proved too deadly for the visitors, bundling them out for 121.
Mathews has been continually troubled by injuries and has played just one game since being reappointed as Sri Lanka's limited-overs captain in January.
Mathews will take the reigns of the team in the upcoming tri-nation One Day International tournament in Bangladesh.
The SLC sources said the new head coach Chandika Hathurusinghe is focused on the 2019 World Cup and wants a permanent solution to the captaincy problem.
The injury means Mathews will also remain doubtful for the start of the forthcoming Bangladesh tour.
Matthews, who suffered from cramps during his unbeaten century knock in the second ODI at Mohali on December 13, bowled and batted as the Sri Lanka cricket team hit the ground during the training session in Visakhapatnam on Friday.
India bowled 85.3 overs on the day and not for once was play stopped due to players complaining about pollution.
Mathews thanked batting coach Thilan Samaraweera for helping him sort out some technical glitches that had crept into his batting.
Mathews is yet to score a Test hundred since August 2015 and in that phase, he has aggregated 917 runs in 32 innings at 28.65 with his overall average slipping to 44.93 from 52.06.
Since making his Test debut in 2015, 22-year-old Mendis was being seen as the best batting prospect for Sri Lanka after the retirement of Kumar Sangakkara and Mahela Jayawardene.
The hosts were struggling at 154/5 in reply to India's mammoth first innings total of 600 at the end of second day's play in the first Test at Galle.
The left-hander says India will be too good for Sri Lanka on the tour, beginning with the first Test from July 26 in Galle.
Sri Lanka trail by 63 runs as Zimbabwe's skipper Cremer picked up three crucial wickets on Day 2 to put visitors ahead.
Sri Lanka Cricket has named Dinesh Chandimal as the new test captain while opener Upul Tharanga will be in charge of the team in the shorter formats.
Sikandar Raza starred with both the bat and ball to help Zimbabwe edge out Sri Lanka by three wickets and clinch a historic series victory in the fifth One-day International.
India will take on hosts Sri Lanka in the first Test on July 26 at the Galle International Stadium, Galle.
With the win, the hosts have levelled the series 1-1 after Zimbabwe won the first match by six wickets.
Sri Lankan fielders dropped Sarfraz Ahmed twice off Lasith Malinga's overs as the Pakistan skipper cracked a match-winning 61 to take his team to the semi-finals.
Captain Angelo Mathews termed Sri Lanka's record win over India as one of their top victories.
India's unexpected loss to Sri Lanka has turned the remaining Group B matches into virtual quarterfinals: India vs top-ranked South Africa on Sunday, followed by Sri Lanka vs Pakistan on Monday.
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