Almost 50,000 people had flooded the basilica to pay homage to the late pontiff, laid out since Wednesday in an open coffin before his funeral on Saturday, Vatican media said.
Dedicated mourners queued overnight and given the size of the crowds, the church, which was initially scheduled to close at midnight, was kept open until 5.30am before it reopened at 7am.
The body of the 88-year-old pontiff, who died on Monday in his rooms at the Vatican's Santa Marta guesthouse after suffering a stroke, was brought to St Peter's in a solemn procession on Wednesday.
Francis, a groundbreaking reformer, had an often turbulent 12-year reign in which he repeatedly clashed with traditionalists and championed the poor and marginalised.
On Saturday, more than 170 delegations including heads of state and government are expected in St Peter's Square for the funeral ceremony, with millions more  watching on television across the globe.
"A chapter in the Church's history has been closed," Cardinal Gerhard Ludwig Muller told Italian daily la Repubblica in an interview published on Thursday.
The German cardinal, known to be a conservative and one of the 133 princes of the church expected to hold a conclave next month to elect the church's 267th pontiff and successor to Francis, said there was "unanimous appreciation" for the Pope's work on migrants and the poor.
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