The pontiff, aged 86, was earlier flown by helicopter from the Vatican to his retreat at Castel Gandolfo, near Rome.
His deputy, Cardinal Tarcisio Bertone, is now in charge of the world’s 1.2 billion Roman Catholics until a new pope is elected next month.
Benedict vowed “unconditional obedience and reverence” to his successor.
He stepped down after nearly eight years in office – the first pontiff to do so in 600 years.
Benedict officially ceased to be the Pope at 20:00 local time.
The resignation was marked by the papal Swiss Guards stepping down from their posts at Castel Gandolfo to return to the Vatican. The protection of Benedict was taken over by Italian police.
In his retirement, Benedict will wear a simple white cassock rather than his papal clothes, and swap his famous red shoes – the color is symbolic of the blood of the early Christian martyrs – for brown.
His “Fisherman’s Ring”, the special signet ring which contains the Pope’s name and is impressed to validate certain official documents, is expected to be destroyed along with the lead seal of the pontificate.
The German pontiff, who was born Joseph Ratzinger, will continue to be known as Benedict XVI, with the new title of “pope emeritus”.
The long-time theologian is expected eventually to retire to a monastery on a hill inside Vatican City, with officials saying he will not be able intervene publicly in the papacy of his
successor, though he may offer advice.
The conclave of 115 cardinals is expected to meet at the Vatican on Monday morning to start planning the election of the next pope.
Earlier on Thursday, bells of St Peter’s rang across the Vatican as Benedict boarded the helicopter for a short flight to Castel Gandolfo.
Before that, the pontiff was greeted for the last time by top officials in the Curia – the administrative body that runs the Holy See.
Benedict then appeared at a window overlooking the public square in Castel Gandolfo to bless a cheering crowd.
“Thank you very much for your friendship,” Benedict said.
“I will simply be a pilgrim who is starting the last phase of his pilgrimage on this earth.
“Let’s go forward with God for the good of the Church and the world.”
Some in the crowd were in tears listening to what could be Benedict’s final public words as pope.
In his final tweet, Benedict wrote: “Thank you for your love and support. May you always experience the joy that comes from putting Christ at the centre of your lives.”
The Vatican now enters the Sede Vacante – or period of transition between two pontificates.
Benedict’s successor must focus on reforming the Vatican bureaucracy which has often been overly hesitant to react to the various crises which have arisen during Benedict’s papacy.
On Thursday morning, the Pope received the cardinals at the Vatican’s Clementine Hall, warmly embracing Cardinal Angelo Sodano, who passed on best wishes on behalf of those gathered.
“Among you there is also the future pope to whom I promise my unconditional obedience and reverence,” the pontiff said.
“The Church is a living being,” he added, but it “also remains always the same”.
In his public farewell speech on Wednesday, Benedict hinted at Vatican infighting.
His decision to resign has been openly criticized by Australia’s top Catholic, Cardinal George Pell, who questioned his leadership skills.
The Church has been beset by scandals over sexual abuse by priests and leaked confidential documents revealing internal corruption and feuding.
An estimated 150,000 people packed into St Peter’s Square on Wednesday to hear Benedict speak in his last address there.
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