"The presence of God today is also called Rohingya," the Pope said after speaking to an interfaith audience in the Bangladeshi capital of Dhaka.
He did not use the term in public earlier in the week in Myanmar, to the dismay of campaigners for the Rohingya, whose stories of escaping violence in the country have provoked international condemnation. Friday is the final full day of his trip.
After his speech, the Pope met a group of Rohingya refugees one by one, giving some of them blessings and listening to the stories of others.
"Your tragedy is very hard, very big. We give you space in our hearts," the Pope said. "In the name of everyone, of those who persecute you, those who hurt you, and especially of the world's indifference, I ask for your forgiveness. Forgive us."
"Many of you talked to me about the great heart of Bangladesh, which offered you refuge. Now I appeal to your heart to give us the forgiveness we are asking from you," he told the group of refugees after meeting them.
More than 620,000 Rohingya have fled across the border from Myanmar to neighboring Bangladesh since a spate of violence began in August. Many say they were forced to flee atrocities committed by the Myanmar military.
Myanmar's government does not use the term Rohingya to refer to the group. It considers the Rohingya people to be illegal immigrants from Bangladesh, even though some families have lived in Myanmar for centuries. The Rohingya are not recognized as an official minority in Myanmar, effectively meaning they are denied citizenship.
During a speech Tuesday alongside Myanmar's de facto leader, Aung San Suu Kyi, Pope Francis did not use the term Rohingya despite hopes he would do so.
Vatican spokesman Greg Burke dismissed the idea that Francis -- who has used the Rohingya term before -- diminished his moral authority by avoiding a direct reference to the group during his visit to Myanmar, the first by a Pope to the Buddhist-majority country.
"People don't expect him to solve impossible problems," Burke said.
Activists argued that because Francis did not use the term while he was in Myanmar, he was complicit in the country's strategy to delegitimize the Rohingya plight by questioning their name and identity.
"The term Rohingya is not a racial slur. It is a dignified term for more than two million people who are living across the world," European-based Rohingya activist Nay San Lwin told CNN in an email.
After the Pope's remarks in Bangladesh, Lwin told CNN that he and other Rohingya advocates felt like "winners."
"Unexpectedly he used the correct term. He didn't avoid when he met the Rohingyas in person," Lwin said.
The international community has been outraged by the stories of fleeing refugees.
Jafar Alam, a 24-year-old Rohingya who was due to speak with the Pope in Bangladesh, told reporters before the meeting that the army lined up 30 people in his village and killed them all.
The United Nations, the US and the UK have accused the Myanmar military of ethnic cleansing, systematically driving the minority Muslim population from their homes through murder, rape and terror.
Myanmar's military claims it is pursuing terrorists responsible for a deadly attack on security forces in August. It denies that it has systematically persecuted the Rohingya.
During his visit to Myanmar, Francis met the country's two most important leaders: Suu Kyi and Senior Gen. Min Aung Hlaing, the commander-in-chief of Myanmar's armed forces.
During a brief meeting with Pope Francis Monday, Hlaing insisted that all faiths were able to worship freely in Myanmar.
But many Myanmar watchers said Hlaing's claim is false, pointing to the Rohingya crisis.
"The mind boggles when you're confronting such blatant falsehoods and incredibly bogus narratives that have been formulated by people covering up atrocities," said Phil Robertson, the deputy director of Human Rights Watch's Asia division.
Suu Kyi, a former Nobel Peace Prize winner for her nonviolent resistance to the military junta that ruled Myanmar for decades, has also denied that ethnic cleansing is going on her country.
She addressed the crisis in general terms during a speech alongside Francis Tuesday, saying her government aims "to bring out the beauty of our diversity and to make it our strength, by protecting rights, fostering tolerance, ensuring security for all."