The late pontiff, who led the Catholic Church for almost eight years before he stepped down in 2013 due to ill health, died on Saturday.
Michelle O’Neill offered condolences to Catholics across Ireland and around the world.
“All those from across our society of a Catholic faith will be saddened by the news that Pope Emeritus Benedict XVI has sadly passing away,” she said.
“As noted by the Archbishop of Armagh, Reverend Dr Eamonn Martin, Pope Benedict had a steadfast interest in Ireland, and our peace process.
“His very significant contribution to theological and academic work, and his thought leadership over many years are widely regarded by both supporters and critics alike.
“I wish to extend my sincere condolences to Archbishop Eamonn Martin, Holy See representative to Ireland, Reverend Monsignor Julien Kabóre, Pope Francis and all members of the Catholic faith here in Ireland, and across the world.”
It comes after the Archbishop of Armagh and Catholic Primate of All Ireland paid tribute to the first Pope to resign from office since 1415.
He said Benedict believed that "peace is built upon respect for life and reaching out to the other, reaching out beyond your own tribe" and hailed him as "probably one of the greatest theologians of our time".
The former Pope is currently lying in state in St Peter’s Basilica.
As daylight broke, 10 white-gloved Papal Gentlemen — lay assistants to pontiffs and papal households — carried the body on a cloth-covered wooden stretcher up the centre aisle to its resting place in front of the main altar under Bernini’s towering bronze canopy.
A Swiss Guard saluted as the body was brought in through a side door after Benedict’s remains had been transferred from the chapel of the monastery grounds where the frail 95-year-old died on Saturday morning.
The German cleric’s longtime secretary, Archbishop Georg Gaenswein, and a handful of consecrated laywomen who served in Benedict’s household, followed the van by foot in a silent procession towards the basilica.
Thousands of people have been paying their respects with large queues forming outside in St Peter's Square.
Among the VIPs granted early access were Italian premier Giorgia Meloni and President Sergio Mattarella.
Pope Francis will preside over Thursday's funeral marking the first time a Pope will be buried by his successor.
Archbishop Martin and Archbishop of Dublin Dermot Farrell are among those who will travel to Rome for the Funeral Mass.
The Vatican said only two nations – Italy and Germany – had official delegations with formal invites to the funeral, as Benedict was no longer head of state.
The Catholic Church in Ireland opened a book of condolence in St Patrick's Cathedral in Armagh over the weekend as well as an online version on the Irish Catholic Bishops' Conference website.