Benedict's death on Saturday brought to an end a decade of the former and present pope living side-by-side in the Vatican and it was the first time in more than 200 years that a pontiff had led the funeral service of his predecessor.

His death was a loss for conservatives who yearned for a return to a more traditional Church symbolised by Benedict, who shocked the world in 2013, by becoming the first pope in 600 years to resign instead of reigning for life.

At the end of the funeral in St. Peter's Square on Thursday, some people shouted in Italian "Santo Subito!" (Make him a saint now!). It was the same phrase used at the funeral of Pope John Paul II in 2005, although by many more people then.

While three of the last five popes have been made saints, only around one-third of all pontiffs have been canonised in the Church's 2000-year history.

Francis, who sat for most of the service because of a knee ailment, rose at the end as Benedict's coffin was being carried away. Holding himself up with a cane he touched it while bowing his head in silent prayer.

The service started about two hours earlier when, to the sound of tolling bells, 12 pallbearers carried the wooden coffin holding Benedict's remains out of St. Peter's Basilica and placed it on the ground before the largest church in Christendom.

The last time a reigning pope had presided over the funeral of a predecessor was in 1802, when Pius VII led the service for Pius VI, whose body returned to the Vatican after he died in 1799 in exile.

In his homily read while sitting before the altar, Francis used more than a dozen biblical references and Church writings in which he appeared to compare Benedict to Jesus, including his last words before he died on the cross: "Father, into your hands I commend my spirit."

During the Mass concelebrated by 125 cardinals, 200 bishops and about 3700 priests, Francis spoke of the "wisdom, tenderness and devotion that he bestowed upon us over the years".

He mentioned Benedict by name only once, in the last line, saying: "Benedict, faithful friend of the Bridegroom,(Jesus) may your joy be complete as you hear his voice, now and forever!"

Clergy from around the world, a handful of heads of state and thousands of faithful attended the ceremony as the sun slowly broke through the fog.

More than 1000 Italian security personnel were called up to help safeguard the event, and air space around the tiny Holy See was closed off for the day. Italy ordered that flags around the country be flown at half staff.

Italian police said about 50,000 people were in the square.

People from all over the world, many from Benedict's native Germany, arrived in the early hours to say farewell to Benedict.

About 200,000 people filed past Benedict's body while it was lying-in-state for three days until Wednesday evening.

An account of Benedict's papacy, along with other items, including Vatican coins minted during his reign, was also tucked into the coffin. The account, written in Latin, says he "fought with firmness" against sexual abuse by clergy in the Church.

After the funeral ceremony, the coffin was taken back inside the basilica to be encased in zinc before being sealed in a second wooden casket.

At his request, Benedict will be buried later on Thursday in the underground Vatican grottoes in the niche where first Pope John XXIII and then John Paul II were interred before their remains were transferred to more prominent places in the basilica above.

― With AAP.