Benedict also gave a final set of instructions to the "princes" of the church who will elect his successor, urging them to be united as they huddle to choose the next pope.
"May the College of Cardinals work like an orchestra, where diversity — an expression of the universal church — always works toward a higher and harmonious agreement," he said.
It was seen as a clear reference to the deep internal divisions that have come to the fore in recent months following the leaks of sensitive Vatican documents that exposed power struggles and allegations of corruption inside the Vatican.
The audience inside the Apostolic Palace was as unique as Benedict's decision to quit, with the pope, wearing his crimson velvet cape and using a cane, bidding farewell to his closest advisers and the cardinals themselves bowing to kiss his fisherman's ring for the last time.
A few hours later, Benedict's closest aide, Monsignor Georg Gaenswein, wept by his side as they took their final walk down the marbled halls of the Apostolic Palace to their motorcade that took them to the helipad at the top of a hill in the Vatican gardens.
As bells tolled in St. Peter's and in church towers across Rome, Benedict took off in a helicopter that circled St. Peter's Square, where banners reading "Thank You" were held up skyward so he could see. He flew to Castel Gandolfo, where he has spent his summers enjoying the quiet gardens overlooking Lake Albano.
Around the time he took off, the Vatican sent a final tweet from Benedict's Twitter account, (at)Pontifex. "Thank you for your love and support. May you always experience the joy that comes from putting Christ at the centre of your lives."
Soon afterward, that tweet and all Benedict's previous ones were deleted and the profile was changed to read "Sede Vacante."
And a few seconds past 8 p.m., the soft click of the 20-foot-high wooden door at Castel Gandolfo closed, signaling the end of the papacy. A Vatican official was then seen taking down the Holy See's white and yellow flag from the Castel Gandolfo residence.
"We have the pope right here at home," said Anna Maria Togni, who walked two kilometers (one mile) from the outskirts of Castel Gandolfo to witness history. "We feel a tenderness toward him."
Benedict set his resignation in motion Feb. 11, when he announced that he no longer had the "strength of mind and body" do to the job. It was the first time that a pope had resigned since Pope Gregory XII stepped down in 1415 to help end a church schism.
In the weeks since Benedict's announcement, speculation has mounted whether other factors were to blame. By the time his final day came around though, Benedict seemed perfectly serene with his decision.
The Vatican spokesman, the Rev. Federico Lombardi, said the pope's pledge to obey his successor was in keeping with his effort to "explain how he intends to live this unprecedented situation of an emeritus pope."
"He has no intention of interfering in the position or the decisions or the activity of his successor," Lombardi said. "But as every member of the church, he says fully that he recognizes the authority of the supreme pastor of the church who will be elected to succeed him."
The issue of papal obedience is important for Benedict. In his last legal document, he made new provisions for cardinals to make a formal, public pledge of obedience to the new pope at his installation Mass, in addition to the private one they traditionally make inside the Sistine Chapel immediately after he is elected.
The Rev. Thomas Reese, author of "Inside the Vatican," a guide to the Vatican bureaucracy, welcomed Benedict's similarly public pledge, saying: "There is room in the church for only one pope and his pledge of obedience shows that Benedict does not want to be used by anyone to undermine the authority of the new pope."
He said he would have preferred Benedict to go back to his given name and eschew the white of the papacy.
"Symbols are important in the church," he said.
Winfield reported from Vatican City.
Follow Nicole Winfield at www.twitter.com/nwinfield
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