During his public addresses on the previous leg of his trip in mainly Buddhist Myanmar, Francis never referred to the group by name or directly alluded to the crisis in Rakhine state, from where over 620,000 Rohingya have fled over the Myanmar-Bangladesh since August.
He spent nearly an hour answering reporters' questions after his six-day trip to Myanmar and Bangladesh, but insisted that most of the questions be about the trip.
The Senior General's Facebook post about the meeting said the Snr-Gen explained to the Pope that there was no religious discrimination in Myanmar as the country ensures religious freedom.
But Yangon-based analyst David Mathieson said the tour would "do nothing dramatically to alter the humanitarian disaster of Rakhine" in Myanmar, where the violence against the Rohingya has unfolded. "I dared to say everything I wanted to say".
"I knew that if, in an official speech, I would have used the word, they would close the door in my face", the Pope told reporters who asked why he did not name the group.
He said: "It's true I didn't have the pleasure of slamming the door in their face publicly with a denunciation".
One refugee expressed gratitude that the pope had finally uttered the word Rohingya, and said he believed the meeting would have a big impact.
Pope Francis prays with Rohingya refugees during an interfaith peace meeting in the garden of the Archbishop of Dhaka's residence in Bangladesh's capital on Friday. I still bleed, there is pain in the abdomen, my back hurts, I get headaches. I yelled a bit.
He had a few minutes with each of them, listening to their stories with the help of an interpreter, holding their hands and looking into their eyes.
"I will share my pain with him", she added, Reuters reported.
Listening to them was emotional, he said, and "I couldn't let them leave without saying something" to them. He also apologised for all they had suffered. Francis said they deserved to hear something from him directly, and so he asked for a microphone and spoke from the heart.
Human rights groups have criticised Burma's de facto civilian leader Aung San Suu Kyi, a Nobel Peace Prize victor who was under house arrest for a total of 15 years, for not taking a stand against the generals.
"Myanmar is a nation that is growing politically, in transition", Francis said in response to a question about Suu Kyi and budding democracy in Burma.
This photo combo of two images show Pope John Paul II riding in a three-wheeled bicycle rickshaw at the Vatican Mission in Dhaka, Bangladesh, during his one-day visit to the city, on November 19, 1986, on left and Pope Francis riding a traditional Bangladesh rickshaw as he arrives at an interfaith and ecumenical meeting for peace in the garden of the archbishop's residence, in Dhaka, Bangladesh, Friday, Dec. 1, 2017.