The white-domed mosque, the largest in Southeast Asia, is less than half a mile from Indonesia's presidential palace in the center of Jakarta.
The official Antara news agency said the blast took place about 3 p.m. at the Istiqlal Mosque. Three witnesses told police they saw two men on motorcycles speeding away from the scene immediately after the explosion, Antara reported.
Iman Budiman, who works at the mosque, said the explosion was in the basement, which holds several offices.
At least 15 rooms were damaged, some pillars inside the mosque were cracked and dozens of windows were smashed, he said.
Scores of people who had been reading the Koran, Islam's holy book, fled one of the damaged rooms, Budiman said.
Antara said the explosion occurred in front of an office occupied by the Indonesian Ulemas Council. The council represents thousands of Islamic preachers and is one of the country's most influential religious bodies.
About 90 percent of Indonesia's 210 million people are Muslim, making it the world's most populous Islamic nation.
The explosion follows months of escalating religious violence between members of the country's Muslim majority and its Christian minority.