Pope Francis prayed for his predecessor’s passage to heaven as he presided over a special New Year’s Day Mass in St Peter’s Basilica on Sunday, a day after Pope Emeritus Benedict XVI died in retirement at the Vatican.

The huge basilica will host Benedict’s coffin from Monday, and thousands of faithful are expected to attend the first of three days of viewing.

Benedict, 95, died on Saturday morning in the Vatican where he had lived since retirement. He was the first pope in centuries to resign, citing his increasing frailty.

On Sunday, Benedict’s body lay on a burgundy-coloured bier in the chapel of the monastery. He was dressed in a mitre, the headgear of a bishop, and a red cloak-like vestment. A rosary was placed in his hand.

Behind him – visible in photos released by the Vatican – was the chapel’s altar, and a decorated Christmas tree.

Francis looked weary and sat with his head bowed as Mass began on the first day of the year, an occasion the Catholic Church dedicates to the theme of peace.

He departed briefly from reading his homily, with its emphasis on hope and peace, to pray aloud for Benedict.

“Today we entrust to our Blessed Mother our beloved Pope Emeritus Benedict XVI, so that she may accompany him in his passage from this world to God,” he said.

The pontiff will lead Benedict’s funeral on Thursday in St Peter’s Square.

That rite will be a simple one, the Vatican has said, in keeping with the wishes of Benedict, who for decades as a German cardinal had served as the Church’s guardian of doctrinal orthodoxy before he was elected pope in 2005.

Francis went to pay his respects to Benedict immediately after the retired pontiff died, after receiving a call from the Rev Georg Gaenswein, Benedict’s long-time secretary.

Vatican spokesman Matteo Bruni said Francis stayed in Benedict’s monastery for quite some time before returning to the hotel that serves as his home, across the Vatican Gardens.

In the last few years, Francis has hailed Benedict’s decision to become the first pope to resign in 600 years and has made clear he would consider such a step himself.

Crippled by knee pain, the 86-year-old arrived in the basilica in a wheelchair on Sunday, before taking his place in a chair for the Mass, which was being celebrated by the Vatican’s secretary of state.

Francis, who has repeatedly decried the war in Ukraine and its devastation, recalled those who are victims of war, passing the year-end holidays in darkness, cold and fear.

“At the beginning of this year, we need hope, just as the Earth needs rain,” he said.