Residents fled to higher floors as up to a metre of water inundated streets and homes, also causing traffic chaos in the city of more than 10 million people.
The deluge sparked fears of a repeat of flooding early last year in Jakarta and surrounding areas, which killed more than 60 people and forced around 300,000 from their homes.
There were no immediate reports of casualties in the latest flooding, although water levels reached waist height in several areas of west and south Jakarta, according to local reports.
At least 10,000 homes were swamped on Thursday, a spokesman for the Jakarta governor's office told the Associated Press news agency.
Last year's floods were blamed on the deforestation of mountains to the south of Jakarta and city officials stealing money earmarked for flood prevention schemes.
Drains and rivers blocked with rubbish were also cited as a factor.
With its tropical climate, Jakarta is often affected by flooding.
"It happens every rainy season. I have to move my belongings to the second floor otherwise I will be left destitute," a west Jakarta local said.