Inside the basilica, ushers moved the massive crowds down the marble aisles quickly and many pilgrims said they were surprised their farewell had passed in a flash.
Meanwhile, in a break from tradition the Vatican said yesterday that John Paul II was not embalmed, only “prepared” for viewing.
Vatican spokesman Joaquin Navarro-Valls did not elaborate on the procedure, but an embalmer in Rome said it appeared John Paul’s remains were only touched up with cosmetics.
Massimo Signoracci, whose family embalmed three other Popes, said he could not be certain what had been done without examining the body.
Mr Signoracci said even a light embalming is necessary for a body that is exposed for several days.
John Paul died on Saturday and his remains were put on public view late Monday on an open platform in St Peter’s Basilica. He will be buried Friday.
Historically, organs were removed to make embalming more durable. Relics of 22 Popes - from Sixtus V, who died in 1590, to Leo XIII, who died in 1903 - are kept in Rome’s St Anastasio and Vincent Church, near the Trevi fountain.
Pope Pius X, who reigned from 1903 to 1914, abolished the custom of removing organs.
Embalming usually consists of draining the blood and other bodily fluids and intravenously injecting formaldehyde and other preserving liquids.
Mr Signoracci said his family had embalmed the remains of John XXIII in 1963 and of Paul VI and John Paul I, who both died in 1978.
Paul VI was only lightly embalmed before his body was placed before the public during Rome’s hot summer. But after two days the skin and fingernails began losing their colour.
John XXIII’s body, by contrast, was in excellent condition when it was exhumed from the cramped grotto under the basilica in 2001 - 38 years after his death - and moved to the main floor following his beatification.
Federica Marinucci relived the moment with a video she took inside the basilica using her mobile phone camera.
“Security keeps telling you: ‘Go, go, go,”’ she said. “There wasn’t time to say a prayer.”
The 29-year-old said she had hoped to camp out on the piazza in an overnight vigil, but police had blocked off most of the square to set up wide metal barricades through which the crowds moved toward the church.
People no longer had access to the impromptu shrines covered with farewell letters, candles, stuffed animals and flowers left since John Paul’s death on Saturday.
The line snaked through the piazza, down the wide modern boulevard leading to the Vatican and into the shady side streets nearby.
To make the wait more bearable, the Vatican broadcast prayers and hymns using giant screens and speakers posted along the boulevard.
“Look at me, I don’t need a rest,” said Alviana Tuzi, 73, smiling broadly. She was about half the way to St Peter’s after standing in line for four hours.
“I’m doing this from the heart. Let’s hope we make it.”
John Paul will be laid to rest on Friday in the crypt of St Peter’s, alongside Popes of centuries past near the traditional tomb of the first Pope, St Peter.
Some predict the number of pilgrims in the days leading to the funeral may match the Rome’s own three million residents.