Malta's archbishop led the service at a chapel just a few hundred metres from the site where the anti-corruption blogger was blown up by a car bomb last week.
"Whoever killed Daphne Caruana Galizia wanted to scare and terrorise us," Archbishop Charles Scicluna told the congregation.
"What happened last week was intended to make us fear."
The mass started at 3pm (1300 GMT), the time of her death one week ago, with former presidents, former prime ministers and members of parliament among those attending.
The ceremony came after Pope Francis sent a rare letter of condolence to Malta saying he was praying for Caruana Galizia's family and the Maltese people -- an unusual gesture from the Vatican on the death of a private citizen.
Flowers, cards and the national flag have also been placed at the scene of the explosion.
"Your pen is mightier than Semtex. What you wrote and what you uncovered cannot be blown away," said one message.
The 53-year old blogger had made repeated and detailed corruption allegations against Prime Minister Joseph Muscat's inner circle, and had recently turned her investigative scrutiny on the leader of the opposition as well.
Caruana Galizia's sons were conspicuous by their absence.
After her death they accused Muscat of filling his office with crooks and creating a culture of impunity that turned Malta into a "mafia island".
"Our resolve today is that where there is violence we will work for peace, where there is hatred we work for love, where there is injustice we strive for justice, where there is fear we work for courage," Archbishop Scicluna said.
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