Vice National Police Chief Syafruddin, who uses one name, said an initial investigation showed that the suspected suicide bomber had also died in the blast.
The explosion occurred Wednesday evening in a parking lot next to the bus terminal in the Kampung Melayu area of easter Jakarta. The injury toll was unclear, with broadcaster TV One reporting that two civilians including a female student had been wounded.
A police bomb squad was investigating the explosion.
Indonesia, the world's most populous Muslim country, generally follows a moderate form of the faith.
TV pictures showed smoke rising from the terminal and police rushing to carry casualties away from the scene. Large numbers of police officers were at the scene and had cordoned it off.