The six were among about 251 hostages taken from southern Israel during Hamas's unprecedented October 7 attack, which triggered the ongoing war.
Of them, 97 hostages are still held in the Gaza Strip, including 33 the Israeli military says are dead.
"I think of the Middle East. So many innocent victims. I think of the mothers who have lost sons to war. How many young lives cut short," Francis said at the end of the Angelus prayer.
"I think of Hersh Goldberg-Polin, found dead in early September with five other hostages in Gaza.
"In November last year, I met his mother, Rachel, whose humanity struck me. I accompany her at this time. I pray for the victims and continue to be close to all the families of the hostages," he added.
Goldberg-Polin, an Israeli-American national, was 23 when he was abducted from a music festival.
He sent his mother Rachel a text message saying "I love you" followed by another saying "I'm sorry".
A Hamas video from the day showed him being loaded onto a pick-up truck with part of his left arm missing. It had been blown off in the attack.
"Let the conflict in Palestine and Israel cease. Let the violence cease. Let the hatred cease. Let the hostages be released. Let negotiations continue. And may solutions for peace be found," Francis said.
Hamas's October 7 attack resulted in the deaths of 1,205 people, mostly civilians, according to an AFP tally based on Israeli official figures.
Israel's offensive has killed at least 40,738 people in Gaza, according to the Hamas-run territory's health ministry. The UN rights office says most of the dead are women and children.
The fighting has devastated Gaza, repeatedly displaced most of its 2.4 million people and triggered a humanitarian crisis.
