Ade Jantra of Persija scored the single goal for his team in the 12th minute, while the goal for Papua was scored by James Koko Lomel in the 18th minute through a penalty shootout.
The tournament was officially opened by President Joko Widodo (Jokowi) by kicking off the first game in Jayapura, Papua Province on Friday night.
The tournament was held at the Papua provincial stadium of Mandala Jayapura, and participated in by 18 clubs.
The opening ceremony of the event was also attended by Defense Forces (TNI) commander General Gatot Nurmantyo, the National Police Chief General Badrodin Haiti, and Youth and Sports Minister Imam Nahrawi.
The soccer event, scheduled from April 29 to May 29, 2016, will be held in 16 different cities.
The participating clubs are Arema Cronus FC, Bali United, PS Barito Putera, Bhayangkara Surabaya United, Madura United, Mitra Kukar FC, Persegres, Persela Lamongan, Persib Bandung, Persija Jakarta, Perseru Serui, Persipura Jayapura, Persiba Balikpapan, PS TNI, PSM Makassar, Pusamania Borneo FC, Semen Padang FC and Sriwijaya FC.