The leader of the world's Roman Catholics urged reconciliation and "respect for each ethnic group and identity," but did not specifically mention the Rohingya and their plight.
Standing alongside Suu Kyi, Francis spoke mostly in general terms. The highly-anticipated remarks will likely please his hosts but may draw condemnation from human rights activists, who blame the Myanmar army for driving out hundreds of thousands of Rohingya from the country.
Francis did not specifically address allegations of ethnic cleansing but said religion has an important role to play in solving the crisis.
"The arduous process of peace-building and national reconciliation can only advance through a commitment to justice and respect for human rights," he said, according to a translation provided by the Vatican.
Suu Kyi also spoke in mostly in generalities, though she mentioned the location of the crisis by name.
"As we address long standing 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 endeavors has been invaluable," she said.
Suu Kyi and Francis met briefly before the speeches.
Mass exodus
More than 620,000 Rohingya have fled across the border to neighboring Bangladesh since a recent spate of violence began in August. Refugees allege the Myanmar's military has murdered children, raped women and razed villages.
Burmese authorities deny the accusations. They say they are targeting militants responsible for killing security personnel after co-ordinated attacks on police posts in August.
Francis is expected to meet with Rohingya Muslims who fled their homes and are surviving in crowded refugee camps when he visits Bangladesh later this week.
"Myanmar has been blessed with great natural beauty and resources, yet its greatest treasure is its people, who have suffered greatly, and continue to suffer, from civil conflict and hostilities that have lasted all too long and created deep divisions," Francis said.
"As the nation now works to restore peace, the healing of those wounds must be a paramount political and spiritual priority. I can only express appreciation for the efforts of the Government to take up this challenge," he said.
Experts noted that, during his visit, Pope Francis has the precarious and risky task of balancing the humanitarian, diplomatic and religious quagmires that have plagued Myanmar for decades.
Despite hinting at the Rohingya crisis throughout his speech, Pope Francis reiterated the message from the Vatican that the main purpose of his visit was "to pray with the nation's small but fervent Catholic community, to confirm them in their faith, and to encourage them in their efforts to contribute to the good of the nation."
The visit comes six months after formal relations were established between the Holy See and Myanmar.
The name he wouldn't say
The Rohingya have long faced persecution in Buddhist-majority Myanmar. Government and officials do not use the term Rohingya to refer to the minority; they consider them illegal immigrants from Bangladesh, though some families have lived in Myanmar for centuries.
The Rohingya are not recognized by the government as an official minority, meaning they are effectively denied citizenship.
Declining to use the word "Rohingya" was effectively a win for those trying to delegitimize the term, said Penny Green, a professor of law at Queen Mary University of London who studies the Rohingya conflict.
She told CNN in an email the decision is "a clear concession to the Myanmar regime and its Christian mouthpiece Cardinal Bo who have been at pains to remove the Rohingya identity, not only from the country but also from the national lexicon.
"Pope Francis's talk of universal human rights, peace and dignity is little more than platitude," Green said. "If the Pope cannot even mention the name of those who have been most cruelly and comprehensively excluded then it says little for any moral pressure he was hoping to apply to Aung San Suu Kyi and the military regime she has aligned herself to."
Suu Kyi speech
"Of the many challenges that our government has been facing, the situation in the Rakhine has most strongly captured the attention of the world," Suu Kyi said. "It is the aim of our Government to bring out the beauty of our diversity and to make it our strength, by protecting rights, fostering tolerance, ensuring security for all."
Suu Kyi has been harshly criticized by Western leaders for not doing more to stymie the army's security operations or speak out on behalf of the Rohingya.
Rohingya activists hoped she would use her moral authority as a Nobel Peace Prize laureate -- an award she won for her nonviolent resistance to the military junta that formerly ruled the country -- to take up the issue, despite its political unpopularity in the Buddhist-majority Myanmar.
Her Tuesday speech touched upon the issue in general terms.
"We today who have been given the opportunity to effect changes that could open new vistas of progress for our nation, will strive to discharge our duties with probity and humility," she said.
Religions working together
Pope Francis said it is a "great sign" that leaders of various religions have begun working together.
"Religious differences need not be a source of division and distrust, but rather a force for unity, forgiveness, tolerance and wise nation-building," Francis said. "The religions can play a significant role in repairing the emotional, spiritual and psychological wounds of those who have suffered in the years of conflict."
After the meeting, which had originally be scheduled for Thursday, Senior Gen. Min Aung Hlaing said all faiths in the country are able to worship freely.
"The Tatmadaw is making efforts to restore peace, and wish of all Tatmadawmen is to ensure peace of the nation," he said, using an alternative name for the country's army. "Myanmar has no discrimination among the ethnics."
Myanmar's military still holds the balance of power in the country after its transition to partial democracy in 2015. The army oversees security operations, included those blamed for sparking the refugee exodus of refugees, for which it does not answer to the civilian-elected government.
Under the country's constitution -- crafted by a military junta before it handed over power to a mostly-civilian government -- the generals still control the security forces, the police and key cabinet positions. It also included a clause barring Suu Kyi from running for president. When her party swept to power in the 2015 election, a special position -- State Counselor -- was created for her.