The ICC stated that the player breached the 'Code of Conduct' by changing the condition of the ball by unfair means.
He becomes the third captain in recent times to be charged with ball-tampering after Faf du Plessis and Steve Smith.
ICC regulations see a match ban and fine for such incidents, but the punishment could be increased as well.
How did the incident unfold?
On-field umpires Ian Gould and Aleem Dar found the Lankan players guilty of shining the ball using 'unfair' means. The officials decided to change the ball, besides levying a 5-run penalty. West Indies saw their 1st innings total surge to 123/2 from 118/2.
Know all about the drama
Due to umpires' decision, the Sri Lankan players refused to take the field on Day 3 of the Test.
Chandimal was seen having a long discussion with the umpires and led the team out of the field.
The Lankan officials discussed the whole incident with match referee Javagal Srinath.
SLC released a statement later on denying any wrongdoing by their players.