The 142-km (88.23-mile) railway, one of the president's flagship infrastructure projects and part of China's Belt and Road Initiative has faced problems ranging from land procurement issues, pandemic-related delays and ballooning costs.
Monday's launch for the bullet train named "Whoosh" is far behind the original target of operations in 2019.
"The name is inspired by the sound of a rushing high-speed train," Jokowi, as the president is popularly called, said during the launch.
The maximum operating speed of the train could reach 350 km per hour (217 mph), Jokowi said, calling this "the modernization of our mass transportation that is environmentally friendly".
Luhut Pandjaitan, a senior minister overseeing the project, said at the launch that free trial rides on the bullet train, which have been underway since the second week of September, will be extended and ticket prices will be implemented in mid-October.
A consortium of Indonesian and Chinese companies built the railway.