During the 30 minute audience, Trudeau was expected to ask the Pope for a formal apology for the role the Catholic Church played in Canada's residential school system when indigenous children were removed from their parents and sent to such schools where many allegedly suffered neglect and abuse.
The Pope - himself no stranger to the cause of social justice, he noted to Trudeau - seemed open to the idea, the prime minister said as he related the broad strokes of their private conversation at the Vatican.
The Truth and Reconciliation Commission, which ran from 2008-2015, called for action on 94 points, one of which was an apology from the Catholic Church. Critics of the schools have argued that the institutions were part of an attempt to destroy native tribal cultures.
He added that he stressed to the pope "how he could help by issuing an apology".
"He reminded me that his entire life has been dedicated to supporting marginalized people in the world", Trudeau told reporters.
The leaders "focused on the themes of integration and reconciliation, as well as religious freedom and current ethical issues", the Vatican said.
During the visit, Trudeau extended an invitation to Pope Francis to visit the country of Canada, during which time he could bring the Church's apology for harm done to indigenous people in Canada in the mid-19th through 20th centuries when 150,000 children from native tribes were forced to undergo "enculturation" to the state through attendance at residential schools.
Perry Bellegarde, the National Chief of the Assembly of First Nations, agreed that it would mean a lot to residential school survivors to hear an apology from the head of the Catholic church, especially if it was offered Canada.
The prime minister gave the Pope a rare set of Jesuit Relations books, which have become an important source detailing the beginnings of Canada.
Trudeau said he and the pope also discussed climate change. Both meetings yielded images of the pope standing blank-faced beside each leader, though he is shown smiling broadly at other points during the respective visits.
In return, the Pope gave the prime minister a gold medal marking the fourth year of his pontificate, an autographed copy of his message for World Peace Day and three papal letters about family, the environment and evangelism. The body had recommended that the Pope apologise on Canadian soil for the Church's involvement in the treatment of Canadian Aboriginal children who were subjected to physical violence, derogatory language, neglect and meagre food within a church - and later government - run residential school system.
A spokesperson said Trudeau had a private drink with former prime minister Matteo Renzi on Monday evening.