He urged respect for "each ethnicity and its identity" during a speech in the southeast Asian country, but stopped short of making specific reference to what the UN has labelled "a textbook campaign of ethnic cleansing", with more than 620,000 Rohingya having fled Myanmar's Rakhine state amid a military crackdown in recent months.
The pontiff waited until he was in Bangladesh on Friday before even mentioning the persecuted Muslims by name.
However, he told reporters aboard the papal plane on Saturday that he was confident his message had been heard during private meetings with Myanmar's leader Aung San Suu Kyi and military chief Min Aung Hlaing.
:: Explained: The Rohingya refugee crisis
He said: "It's true I didn't have the pleasure of slamming the door in their face publicly with a denunciation. But I had the satisfaction of dialogue, and letting the other side dialogue, and in this way the message arrived.
"I didn't negotiate the truth, I did it in such a way that he understood that it's not viable to redo today the way things were done in the past. It was a good meeting. Civilised. And even there, the message arrived."
Following talks with the Pope, Ms Suu Kyi referred to the Rohingya crisis as "the situation in the Rakhine state" which had "captured the attention of the world".
:: Pope urges forgiveness for ethnic violence
She has received international condemnation for a failure to speak out over Asia's worst refugee crisis in decades, but the pontiff appeared to have sympathy for her position, as the Nobel Peace Prize winner has no power over the generals her government shares power with.
As it undergoes a political transition following decades of military dictatorship, the Pope said it was possible that Myanmar would make "two steps forward, one step back" as it progressed.
"The possibilities have to be viewed through this optic," he added of the country, formerly known as Burma.
Last month Sky News broadcast the first independent evidence from Myanmar's Rakhine State, laying bare the shocking deprivation and desperation among the thousands of stranded Rohingya.
Some of those who managed to make it to Bangladesh were able to meet the Pope in Dhaka during his Friday visit, during which he shed a tear as he heard their stories and pronounced their name publicly for the first time.