He called on Myanmar's government to ensure "justice and respect for human rights"
Pope Francis avoided referring to the Rohingya by name as he delivered a speech in Myanmar, which has faced claims of ethnic cleansing and genocide against the minority Muslim group.
But the pontiff urged respect "for each ethnicity and its identity" and called on Myanmar's government to ensure "justice and respect for human rights".
In recent months, more than 620,000 Rohingya have fled Myanmar's Rakhine state to Bangladesh amid a police crackdown which the UN has described as a "textbook example" of ethnic cleansing.
Speaking after a meeting with Myanmar civilian leader Aung San Suu Kyi, Pope Francis said civil conflict and hostilities in the country "have lasted all too long and created deep divisions".
"Religious differences need not be a source of division and distrust, but rather a force for unity, forgiveness, tolerance and wise nation-building," he added.
The head of the Catholic Church has been pressured not to use the term "Rohingya" during his four-day trip to Myanmar and Bangladesh - the group is referred to as Bengalis and illegal immigrants in Myanmar.
Earlier, Aung San Suu Kyi referred to the Rohingya crisis as "a challenge" which had "captured the attention of the world".
She said she aimed to "bring out the beauty of diversity and to make it our strength by protecting rights, fostering tolerance and showing security for all".
The leader added: "As we address longstanding issues, social, economic and political, that have eroded trust and understanding, harmony and cooperation, between different communities in Rakhine, the support of our people and of good friends who only wish to see us succeed in our endeavours, has been invaluable."
Pope Francis will deliver an open-air mass to more than 150,000 Catholics in Yangon on Wednesday, before travelling to Bangladesh where he is expected to meet a group of Rohingya refugees.
Leading charities later warned of exploitation, trafficking and prostitution taking place against vulnerable Rohingya women and children in Bangladeshi camps.
Despite this, Myanmar army chief Min Aung Hlaing has denied allegations of widespread brutality by his forces.
The general met Pope Francis on Monday and told him there was "no discrimination" in Myanmar, adding that the military had maintained "the peace and stability of the country".