Chandimal had earlier led the side to series wins in Bangladesh in ODIs and T20Is.
Mathews, on the other hand, has been continually troubled by injuries and has played just one game since being named as Sri Lanka's limited-over captain in January.
According to reports, the 30-year-old was under rehabilitation in Colombo to get fit, but sustained a calf injury during training ahead of the tri-series.
Mathews has missed 60% in the international fixtures. Since late 2016, he has been absent in eight out of 18 Tests, 24 of 40 ODIs, and 14 of 19 T20s.
The 2018 Nidahas Trophy is scheduled to be held in Sri Lanka from March 6. (ANI)