In a rare reaction by the Catholic leader to the death of a private citizen, Francis said he was "saddened by the tragic death" of Daphne Caruana Galizia.
His message, which also offered prayers for the entire nation, was sent to the Archbishop of Malta, Charles Scicluna.
Ms Caruana Galizia died when an explosive charge detonated while she was travelling in her Peugeot car on Monday afternoon.
The 53 year old was an outspoken critic of politicians - including Malta's Prime Minister Joseph Muscat - and organised crime.
Three of her sons, who believe their mother was targeted for the political nature of her work, called upon Mr Muscat to resign and take political responsibility for "failing to uphold our fundamental freedoms".
The incident is one of six remotely-detonated car bombings to hit Malta during the past two years, none of which have been solved.
Mr Muscat denounced the assassination and suggested a reward to information helping lead to the capture of those responsible of Monday's bombing.