The visit has been on the cards for months, but the pontiff’s health issues had raised questions on whether it would go ahead.
The pontiff, who uses a wheelchair, has suffered increasing health problems in recent years, from knee pain to surgery for a hernia and on his colon.
He is known for his work ethic – he never takes holidays – but has been forced to make concessions to his age and health, including cancelling a trip to UN climate talks in Dubai last year.
Involving more than 30 hours of flight, an eight-hour time difference and a series of meetings and masses, the September trip will represent a major physical challenge.
The government in Indonesia, which has the world’s largest Muslim population, had already announced the pope’s visit last month, describing it as a “special gift” for the country’s Catholics.
In a statement Friday, its foreign ministry said the visit was important “for all religious communities”.
“The visit is also expected to strengthen the message of tolerance, unity and world peace.”
