Pope Leo XIV will close the basilica's bronze doors in a ceremony on Tuesday, just over 12 months after they were opened by his predecessor Pope Francis, who died at the age of 88 in April.
"The entire world came to Rome. Pilgrims arrived from 185 countries" for 35 major events, including a festival for young Catholics and the canonisation of the first millennial saint, Archbishop Rino Fisichella told reporters.
The figures showed the centuries-old institution was still "a dynamic church," he added.
The 2025 Jubilee will also be remembered as a rare two-pope Jubilee. The last time a pope died during a Holy Year was in 1700.
Despite torrential rain outside, thousands of pilgrims streamed through the Holy Door at St Peter's on Monday, many pausing to make the sign of the cross.
By tradition, going through it allows them to benefit from a "plenary indulgence", a type of forgiveness for their sins.
"It's really a grace. And I feel great," said Josie Aguirre, 67, from the Philippines.
"It was emotional, the feeling was really great. The jubilee door is a way to renew people's faith, it brings people together," she told AFP.
Organised by the Church every 25 years, the Jubilee is a period of reflection and penance for the world's over 1.4 billion Catholics.
Around 60 percent of pilgrims who attended came from Europe, while 16 percent came from North America, the Vatican said.
Arrivals from North America rose sharply following the election of Leo XIV, the Church's first US pope, in May last year, it added.
Legacy
Significant areas of Rome were spruced up for the Jubilee, including monuments such as the famous Trevi Fountain.
Critics had warned that the Eternal City could struggle to cope with millions more visitors, when it already suffered from overtourism and patchy public transport.
But Rome Mayor Roberto Gualtieri told journalists that the Italian capital had risen admirably to the occasion in what was a "record year" for tourists.
The Jubilee's "main legacy" was a renewed "confidence in the possibility of improving and transforming the city" after "a very long period of stagnation or even decline", he said.
In addition to St Peter's Basilica, Holy Doors were opened in Rome's three major basilicas during the Jubilee year.
Pilgrim John Yun, 61, a physician from Vancouver, Canada, was disappointed that only one door was still open when he arrived at the Vatican just in time for the end of the Jubilee.
But he and his 21-year-old son made it through and were both looking forward to seeing Pope Leo at the general audience on Wednesday.
"I hope he speaks some English. I love hearing English spoken by the Holy Father," Yun told AFP.
"He seems like he could be my parish priest – he has a very humble face, and he's ordinary. He looks a little awkward. I love it."
The conclusion of the Jubilee is expected to serve as a watershed, allowing Leo to make the papacy fully his own, experts say.
Since his election, the Chicago-born pontiff has published documents prepared by Francis before his death and honoured commitments made by the Argentine, including a trip to Lebanon and Turkey.
"This period has been a 'middle world' in which the old and new pontificates overlapped," the Catholic News Agency's Vatican expert Andrea Gagliarducci wrote on Monday.
"The conclusion of the Jubilee" will allow Leo to "finally assert his leadership beyond the legacy of Pope Francis."
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