Dinesh Chandimal was charged for breaching Level 2.2.9 of the ICC Code of Conduct.
Following concerns raised by umpires Aleem Dar and Ian Gould about the condition of the ball nearing the end of the second day, Sri Lanka were advised before the start of play on Saturday that they could not continue with the existing ball.
Play eventually got under way around 11:30 a.m. after Sri Lanka team management consulted with Sri Lanka Cricket (SLC), and the visitors took the field and continued the match "under protest".
The match referee Javagal Srinath was also seen having an animated discussion with the Sri Lankan team officials.
It's understood one of the main reasons Sri Lanka didn't take to the field was because the umpires only informed them of the ball charge 10 minutes before the start of play, without any footage as evidence.
Five penalty runs have been added to the West Indies total.
Sri Lanka Cricket (SLC) later released a statement denying any wrongdoing by its players.
The Sri Lankan Biard ensured that they "will take all necessary steps to defend any player, in the event any unwarranted allegation is brought against any members of the team".More news: Antoine Griezmann receives heavy criticism for decision video
Match officials charged Chandimal after television footage from the final session's play on Friday appeared to show the captain taking candies out from his left pocket and putting these in his mouth, before applying the artificial substance to the ball which the umpires viewed as an attempt to change its condition.
It was communication with the board in Colombo which finally persuaded Chandimal and his team to continue with the match.
"If there are any, Code of Conduct charges will follow as per usual at close of play", tweeted the ICC.
For West Indies, only opener Devon Smith and wicketkeeper Shane Dowrich posted scores of substance, 61 and 55 respectively. He was shining the ball and had bandages on like many players do.
It was in March that Australia were caught tampering with the ball illegally on the third day of the third Test against South Africa in Cape Town.
Steve Smith and David Warner were stripped of the captaincy and vice-captaincy respectively and banned from playing global cricket for 12 months.
The West Indies resumed on day three on 118-2, which was bumped up to 123/2 by the penalty runs.