"Today during this mass we are paying attention to last Sunday's tragedy and we try to understand it," the cardinal said in a chapel at his residence, where President Maithripala Sirisena and Prime Minister Ranil Wickremesinghe were among the small congregation.
"We pray that in this country there will be peace and co-existence and understanding each other without division," he said.
"What happened last Sunday is a great tragedy, an insult to humanity," he added, calling for prayers for the victims.
The Sri Lankan military is still hunting around 140 Islamic State-linked jihadists, authorities say, and security across the country remains high.
Stuck in time
At exactly 8.45am, the singing of hymns by scores of people outside St. Anthony's church stopped and the bells tolled. The hands on the tower clock are fixed at the time of the blast.
"I come to this church every Sunday, it feels like my second home," said Dharshika Fernando, 19, fighting back tears.
"It feels like people blasted my own home."
Thousands of Sri Lankan troops remained on the streets, guarding churches and mosques for the symbolic day.
Security forces also carried out new arrests, a day after at least 15 people were killed in a raid on a jihadist hideout where suicide bombers blew themselves up.
Police said they arrested two top suspects in connection with the Easter bombings in central Nawalapitiya on Saturday night, taking the total number in detention to more than 100.
Mohamed Saadik Abdul Haq and Mohamed Saahid Abdul Haq, were on a list of six "most wanted" radicals issued on Thursday.
The two men were wanted for the December 26 desecration of Buddha statues at the central town of Mawanella.
That act first brought to attention the National Thowheeth Jama'ath (NTJ) group, which has been blamed for the Easter bombings.
Schools stay closed
The previous night, three men set off explosives killing themselves, three women and six children after a showdown with security forces near the eastern town of Kalmunai.
Police said three other suspected suicide bombers were shot dead by security forces outside the hideout that had been under siege for more than an hour. A civilian was also killed in crossfire.
The Islamic State group, which claimed responsibility for the Easter bombings, said the three men who blew themselves up at Kalmunai were also members of the militant group.
A statement posted by the IS propaganda unit, Amaq News Agency, said the men "clashed with them (Sri Lankan police) with automatic weapons, and after exhausting their ammunition, detonated on them their explosive belts."
Kalmunai is in the same region as the hometown of the jihadist Zahran Hashim who founded the NTJ group.
Another raid in the region targeted a house where authorities said Hashim and the other suicide bombers filmed a pledge of allegiance to IS before staging their attacks.
The video was shown by IS when it made its claim of responsibility.
Footage shown on state television showed explosives, a generator, a drone and a large quantity of batteries inside the converted studio. An IS flag and uniforms were also found, police said.
The firebrand cleric is said to have died in the attack on the Shangri-La, one of three Colombo hotels hit by suicide bombers.
Sirisena used emergency powers to officially ban the NTJ and a splinter group identified as Jamathei Millathu Ibraheem (JMI) on Saturday, his office announced.
In a sign of the tensions, the reopening of schools across Sri Lanka scheduled for Monday has been put back one week. Authorities have also kept up a 10.00pm to 4.00am nationwide curfew.