Kalla and his spouse, Mufidah Kalla, arrived in the largest mosque in Southeast Asia, at 6:45 a.m. local time, and were greeted by Governor of Jakarta Anies Baswedan and Grand Imam of Istiqlal Mosque Nazarudin Umar.
The prayers began at 7 a.m. local time and was led by Imam Ahmad Husni Ismail.
After the prayers, Jusuf Kalla presented a cow for sacrifice to the Mosque management.
Istiqlal Mosque received at least 26 cows, including one each from President Joko Widodo and M Jusuf Kalla, and 17 goats and sheep.
Meanwhile, President Joko Widodo (Jokowi) performed Eid Al-Adha prayers in Cibinong square, Bogor District, West Java Province, Wednesday morning.
The Head of State flanked by Teten Masduki, coordinator of presidential special staff, arrived at the venue at 6:04 a.m. local time.
Acting Governor of West Java Muhammad Iriawan and District Head of Bogor Nurhayanti greeted the President upon his arrival.
KH Zainal Abidin acted as the imam (leader) of the prayers, while after the prayers, DR KH Muhammad Suhendra delivered a sermon.
Following the prayers, President Jokowi handed over a cow weighing 1.3 ton which was donated to Baitul Faizin for sacrifice.
Muslims across Indonesia, and even the world, are celebrating the festival of Eid al-Adha, which coincides with the final rites of the Hajj in Saudi Arabia.
Eid Al-Adha, which means "festival of the sacrifice", commemorates the story of Prophet Ibrahim`s test of faith.
Muslims believe Prophet Ibrahim was ordered by God to sacrifice his son, Ismail. But later God spared the boy, and replaced him with a ram.
The day is marked with the sacrifice of an animal, usually a goat, sheep, or cow, and the distribution of the meat among the poor in particular.
Nearly 90 percent of Indonesia`s population of some 260 million are Muslims. The largest Muslim nation in the world this year sends more than 221 thousand Muslims to perform Hajj pilgrimage in Saudi Arabia.