Appealing for forgiveness and reconciliation, the Pope who visited the Our Lady of Madhu shrine in Mannar, revered by both Sinhalese and Tamil Catholics, called the ethnic communities to "rebuild the unity which was lost" in the conflict with the LTTE, which ended in 2009.
"There are families here today which suffered greatly in the long conflict which tore open the heart of Sri Lanka," the Pope said in a prayer at the church, attended by thousands of worshippers waving the white and yellow Vatican flags.
Thanking Our Lady, the Pope said the Jesus "has the power to heal open wounds and to restore peace to broken hearts."
Several families who suffered during the long conflict were present at the mass the 78-year-old Pope conducted at the shrine.
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The visit is the first by a Pope to the northern Tamil territory.
In July 2008, the statue was removed for safety after the fighting between the LTTE and the government troops intensified.
Madhu, 300 kilometres north of Colombo, was a "no-fire zone" during much of the war and sheltered both Christians and non-Christians fleeing the violence.
It was repeatedly hit by artillery, with Tamil rebels and government forces trading blame for the strikes.
The Pope flew to Mannar after conducting a public mass in Colombo where Indian-origin 17th century Catholic missionary Joseph Vaz was canonised as Sri Lanka's first saint.
Vaz, who was born in 1651 in Goa then a Portuguese colony, went to Sri Lanka in 1687 to minister to the scattered faithful after Dutch colonisers who had seized the island's coastal areas from the Portuguese began persecuting Catholics.
Meanwhile, nearly 700 prisoners lodged in jails across the country were pardoned or released to mark the visit of Pope Francis, the first by a Pope in 20 years.