Cardinal Malcom Ranjith, the archbishop of Colombo, offered a televised Mass from his residence that was attended mostly by priests and nuns.
A letter from Pope Francis addressed to him was read out at the end of the service in which the pontiff said he prayed that "hearts hardened by hatred may yield to His will for peace and reconciliation among all his children."
At St. Anthony's Shrine in Colombo, one of the sites targeted by Easter suicide bombings that killed 257 people, a Mass was celebrated for a small group of children and youth as a means for inner healing.
The Rev. Prasad Harshana said before the Mass that prayers will be offered not only the victims of violence, survivors, Catholics and the country as a whole but also for "those suicide bombers and all those people who are involved in it."
"Because they are also misled by the evil one, we need to pray for the conversion of those people, we pray for the conversion of the hearts of the terrorists, whoever they may be. "
"That is our faith ... we love them all," said Harshana.
The coordinated bombings that targeted three churches and three luxury hotels were carried out by an Islamic State-linked group of Sri Lankan nationals.
Almost all churches remained closed with armed soldiers and police guarding them. Authorities canceled Sunday services after reports emerged that a Catholic church and lay institution could be targeted this weekend.
Catholic schools have also been closed until further notice.
However, all government schools are to reopen Monday for grade 6 and up. Police have announced they will search the premises of all schools Sunday.