"The angels welcome you," Vatican TV said after the announcement came from papal spokesman Joaquin Navarro-Valls.
"The Holy Father, John Paul II, died at 9.37pm (1937GMT) in his private apartment," said his statement.
John Paul died as cardinals led 70,000 people at St Peter's Square in prayers for him in his "last journey".
Bells tolled at the Vatican and across Rome, and Vatican, Italian and European Union flags were lowered to half-staff across the capital.
In a statement issued early on Sunday, the Vatican said the Pope's body was expected to be brought to St Peter's Basilica no earlier than Monday afternoon. The statement did not give a precise cause of death.
The College of Cardinals is to meet at 10am on Monday in its first gathering before a secret election to be held later this month to choose a successor to John Paul II.
The cardinals are expected to set a date for his funeral, which the Vatican said is expected between Wednesday and Friday.
Cardinals from around the world headed to Rome. After the official mourning period for a pope, cardinals hold a secret vote in the Sistine Chapel to choose a successor. Under Vatican tradition, the process will begin within 20 days.
The Pope died after suffering heart and kidney failure following two hospitalisations in as many months.
Pilgrims in the Vatican were
stunned at the Pope's death
Just a few hours earlier, the Vatican said he was in a very serious condition but was responding to members of the papal household.
Cardinal Angelo Sodano, the Vatican's number two official, immediately led the tearful crowd in St Peter's Square in prayers for the dead Pope.
The announcement to the square, by Undersecretary of State Archbishop Leonardo Sandri, silenced the huge crowd. A few minutes later, some people broke into applause in appreciation for the Pope - an Italian tradition among mourners. Others wept.
"Dearest brothers and sisters, at 9.37pm the Holy Father returned to the house of the Father," Sandri said. "We all feel like orphans this evening."
A few people started streaming out of the square, but others stayed and stared at the Pope's windows, where the light still burned.
A seminarian slowly waved a large red and white Polish flag draped with a black band of mourning.
Prelates invited the faithful in the square to keep silent so they might "accompany the Pope in his first steps into heaven".
After the crowd started recovering from a stunned silence, a group of youths started singing: "Hallelujah, he will rise again", while one of them strummed a guitar. Later, pilgrims joined in singing the Ave Maria.
"Dearest brothers and sisters, at 9.37pm the Holy Father returned to the house of the Father. We all feel like orphans this evening"
Archbishop Leonardo Sandri
Concetta Sposato, a pilgrim who heard the Pope had died as she was on her way to St Peter's to pray, said tearfully: "He was a marvellous man. Now he's no longer suffering."
Another pilgrim, Beata Sowa, said: "I'm Polish. For us, he was a father."
From his surprise election in 1978, John Paul II travelled the world frequently, staunchly opposing communism in his native Poland and across the Soviet bloc and preaching against rampant consumerism, contraception and abortion.
A fierce enemy of communism, he set off the sparks that helped bring down communism in Poland, from where a virtual revolution spread across the Soviet bloc. Former Soviet President Mikhail Gorbachev said much of the credit belonged to him.
John Paul II was a robust 58 when the cardinals stunned the world and elected him, a cardinal from Krakow and the first non-Italian pope in 455 years.
He survived a 1981 assassination attempt, when a Turkish man shot him in the abdomen.
In his later years, John Paul II was the picture of frailty, weighed down by Parkinson's disease and crippling knee and hip ailments.
Mourners lingered in St Peter's
Square throughout the night
Although he continued his travels, he was too weak to continue his famous gesture of kissing the ground when he arrived at his destinations.
Hospitalised twice in the past two months after breathing crises, and fitted with breathing and feeding tubes, John Paul II had become a picture of suffering.
He was reported to have had a fever on Thursday night, which the Vatican blamed on a urinary tract infection that later led to the heart and kidney failure.
Navarro-Valls said earlier on Saturday that John Paul II was not in a coma and that he opened his eyes when spoken to.
"He's aware he's passing to the Lord," Cardinal Joseph Ratzinger, one of John Paul's closest advisers, told the Italian bishops' news agency earlier on Saturday.
John Paul II's death set in motion centuries-old traditions. The Vatican chamberlain formally verified the death, which in the past was done by tapping a pope's forehead three times with a silver hammer.
"He was a marvellous man. Now he's no longer suffering"
Pilgrim Concetta Sposato
The Vatican summoned the College of Cardinals, and the Vatican chamberlain destroyed the symbols of the Pope's authority - his fisherman's ring and dyes used to make lead seals for apostolic letters.
The Vatican has declined to say whether he left instructions for his funeral or burial. Most popes in recent centuries have asked to be buried in the crypts below St Peter's Basilica, but some have suggested the first Polish-born pope might have chosen to be laid to rest in his native land.