Hostility, extremism and violence are "betrayals of religion" he told an inter-faith prayer service.
Iraq has been wracked by religious and sectarian violence, both against minorities and between Shia and Sunni Muslims too.
Pope Francis also visited one of Shia Islam's most powerful figures.
Receiving the head of the Roman Catholic Church at his home in the holy city of Najaf, Grand Ayatollah Ali al-Sistani said Christians should be able to live in peace and security like all other Iraqis.
The meeting was seen as a highly symbolic moment in the Pope's visit, which is his first international trip since the start of the coronavirus pandemic more than a year ago, and the first ever papal visit to Iraq.
Covid-19 and security fears have made this his riskiest trip yet.
The 84-year-old leader of the Catholic Church earlier told reporters that he had felt "duty-bound" to make the "emblematic" journey, which will see him visit several sites over four days in Iraq.