Before a Mass at Seoul's Myeongdong Cathedral, Francis prayed with a small number of "comfort women", who were forced to work as sex slaves for Japanese soldiers occupying the country before and during the second World War.
A group of defectors from North Korea and relatives of South Koreans abducted by the North were invited to the mass, which was attended by South Korean President Park Geun-hye.
"Today's Mass is first and foremost a prayer for reconciliation in this Korean family," Francis said, following up on an impromptu prayer on Friday when he urged Koreans to work to unite as one family, "with no victors or vanquished".
The 1950-1953 Korean war ended in an armed truce that leaves North Korea and South Korea in a technical state of war.
North Korea turned down an invitation from the South Korean Catholic church for members of its state-run Korean Catholic Association to attend Monday's Mass, citing the start of joint US-South Korean military drills, also due to begin on Monday.
"Let us pray ... for the emergence of new opportunities for dialogue, encounter and the resolution of differences, for continued generosity in providing humanitarian assistance to those in need, and for an ever greater recognition that all Koreans are brothers and sisters, members of one family, one people," Francis said.
Near the conclusion of Monday's Mass, a choir sang, "Our wish is unification."
One of the "comfort women" who sat in the front row, Kim Bok-dong, gave Francis a small butterfly-shaped pin that he wore on his vestment. The pin is a symbol of their campaign, meant to convey that they want to be liberated and fly in a peaceful and free world, a non-profit group that supports the women said.
About 150,000 to 200,000 Korean women served as Japanese sex slaves, and most lived out their lives in silence; 56 are still alive, according to another nonprofit group. The topic of comfort women has long been a thorn in relations between South Korea and Japan.
South Korea says Japan has not sufficiently atoned for the women's suffering, and has protested against Tokyo's review in June of a landmark 1993 apology, which said that the two countries had worked together on its sensitive wording.
During his trip Francis has reached out to China, with which the Vatican has had fraught relations, and on Sunday said Asian governments should not fear Christians, as they did not want to "come as conquerors" but be integral parts of local cultures. The remarks were intended for communist-ruled countries such as China, North Korea and Vietnam.
The Catholic Church in China is divided into two communities: an "official" Church known as the "Patriotic Association" answerable to the Communist Party, and an underground Church that swears allegiance only to the pope in Rome.
Francis, met by festive crowds, spoke several times during his visit to South Korea about inequality, which has been a theme of his papacy since being elected in March 2013.
South Korea is among the world's wealthiest countries, but is increasingly unequal, with nearly half its elderly living in poverty. South Korea has also seen rapid growth in the Catholic Church, which has doubled in the past 25 years to about 11 percent of the population of 50 million, adding some 100,000 new members each year.