The head of the Roman Catholic Church, who arrived on the tiny island on Monday morning, tossed a wreath into the sea from an Italian coast guard vessel to commemorate the deceased migrants.
Dozens of fishing boats from the island accompanied the coast guard vessel as it pulled into Lampedusa's port.
The pope also met with migrants who have recently arrived on the island after making what is often a dangerous journey across the Mediterranean Sea from North Africa.
This came just hours after a vessel carrying more than 160 people was intercepted by an Italian coast guard patrol boat.
Later, the pontiff celebrated a Mass on the island of just 20 square kilometres (8 square miles), in which he slammed what he described as "the globalization of
indifference" and "the culture of wealth" that causes people to become insensitive to the plights of others.
"We pray for a heart which will embrace immigrants," he said via his Twitter account following the Mass. "God will judge us upon how we have treated the most needy."
Lampedusa, which is closer to Africa than the Italian mainland, has been the point of entry to the European Union for more than 200,000 people since 1999. More than 17,000 would-be migrants have died trying to reach the island during the same time period.
About 4,000 have reached Lampedusa in the first half of this year alone, but this is well below the tens of thousands who reached the island during the Arab Spring revolts of 2011.
The plight of refugees is said to be close to Pope Francis’s heart in part due to his background as the son of Italian parents who emigrated to his native Argentina.
The head of the Vatican’s department for migration, Cardinal Antonio Maria Veglio, told AFP that he hoped the pope’s visit would lead to increased "concrete concern and solidarity to improve situations that have become inhuman and unacceptable."
This is the pope’s first trip beyond the Rome area since taking office in March.
pfd/kms (AFP, AP, dpa)