Ranjan de Silva, a local politician, was shot dead near Colombo late Thursday, hours before the team was due to leave for the three-match Test series in the West Indies.
"There will be no replacement for Dhananjaya," a board official said.
"Instead of a 17-member squad, we will now have 16." Sri Lanka Cricket said it will support the 26-year-old Dhananjaya "at this time of sorrow and grief".
Police said an investigation was underway but no arrests had been made.
Sri Lanka will also miss opener Dimuth Karunaratne who fractured a finger while batting in the nets this month as he prepared for a domestic tournament.
Revised Sri Lanka squad: Dinesh Chandimal (capt), Mahela Udawatte, Kusal Mendis, Kusal Janith Perera, Roshen Silva, Angelo Mathews, Niroshan Dickwella, Rangana Herath, Dilruwan Perera, Akila Dananjaya, Jeffrey Vandersay, Lahiru Gamage, Kasun Rajitha, Suranga Lakmal, Lahiru Kumara, and Asitha Fernando.
First Published: May 25, 2018, 2:48 PM IST