The Asian Tour did not give any details about the date of the tournament, how much prize money would be on offer, sponsors or a venue for the event which they first staged in 1974.
"This agreement marks a new dawn for our national championship," Indonesian Golf Association president Arifin Panigoro said in a statement.
"We are convinced the staging of the Indonesian Open in 2013 and beyond will be hugely successful so that the entire golfing fraternity in Indonesia will be proud of our flagship tournament."
The Asian Tour have been wrestling for events in east Asia with rivals OneAsia, who formed in 2009.
Asian Tour chief executive Kyi Hla Han welcomed the news of the return of the Indonesian Open which will sit alongside their CIMB Niaga Indonesian Masters next year as one of nine confirmed events so far.
"We are excited to have this opportunity to work closely with the PGI and we believe the Indonesian Open is right up there amongst the best of national Opens in Asia," Han said.
"Our players enjoy visiting Indonesia as the golf courses, facilities and hospitality are first class and we look forward to returning for the 2013 Indonesian Open."
The Indonesia Open was the season opener on the OneAsia Tour this year and jointly sanctioned with the Japan Golf Tour Organisation. Australian Nick Cullen won the $1 million title at the Emeralda Golf Club in March.
OneAsia released a preliminary January-May schedule earlier this month with five events including the Indonesia PGA Championship in March.