Jakarta Governor Fauzi Bowo began the event before a carefully selected, invitation-only crowd of several thousand cheering onlookers at the national stadium, but the flame spluttered out after a few seconds and had to be re-lit.
Police earlier broke up a rally by pro-Tibet activists outside the sprawling sports complex, which was closed to the public and protected by hundreds of security forces.
About 100 protesters wearing "Free Tibet" T-shirts were carrying banners reading "No human rights no Olympics" and chanting "A united people will be invincible" when police moved in, dragging nine away for questioning.
All were quickly released at the scene, but a Dutch man was taken to Jakarta police headquarters and remains in custody.
The rally outside the national stadium came three hours ahead of the start of the heavily restricted relay event, which was closed to the public and taken off public roads at China's request, officials said.
Officials had wanted to parade the Olympic flame, on its first ever visit to Indonesia, through the capital's traffic-clogged streets and Chinatown but the plans were changed radically after "coordination" with Beijing.
China has been keen to prevent further embarrassing human rights protests like those that marred previous relay legs in Europe and the United States.
Source: DDNEWS