The 87-year-old pontiff landed at Jakarta's Soekarno–Hatta airport on a chartered ITA Airways flight also carrying his entourage and accompanying reporters.
Francis will also visit East Timor, Singapore and Papua New Guinea over the next 10 days.
Sitting in a wheelchair, Francis disembarked from the plane via a lift and was handed a bouquet of local produce by two children dressed in traditional Indonesian attire.
On a red carpet flanked by honour guards, he was greeted by Indonesia's religious affairs minister, its ambassador to the Vatican and several of the country's bishops, before entering a waiting car, waving and smiling as it drove away.
The ageing pope was not scheduled to attend any public events on Tuesday to allow time for him to rest after a 13-hour overnight flight from Rome.
His first official event will come on Wednesday, when he is due to address Indonesia's political leaders. On Thursday, Francis will take part in an inter-religious meeting at Istiqlal Mosque, the largest mosque in Southeast Asia.
The Asia-Pacific tour will last 12 days in total and is the longest trip yet by the pontiff, who will have travelled nearly 33,000 km (20,505 miles) when he arrives back in Rome late evening on Sept. 13.
The pope, who pushed for the 2015 Paris climate agreement, is expected to continue his appeals to confront the dangers of a warming globe.
Jakarta, the Indonesian capital of at least 10 million people, is vulnerable to the impacts of climate change, with chronic flooding and sinking land. The government is in the process of building a new capital, Nusantara, on Borneo island.
Indonesia, the world's most populous Muslim-majority nation, has about 280 million inhabitants, only about 3% of them Catholic.
Ahead of the Pope's arrival, Indonesian President Joko Widodo said his people warmly welcomed Francis on a visit that had been planned long ago but was delayed by the pandemic.
"This is a very historic visit," he told reporters.
"Indonesia and the Vatican have a similar commitment to cultivate peace and brotherhood as well as ensure prosperity for the people."
