Thousands of residents have been evacuated to temporary shelters, with parts of the capital under four to nine feet (1.2 to 2.7 metres) of water.
Images showed rescuers on rafts battling to evacuate the elderly and children from submerged houses in hard-hit southern and eastern areas of the city, and dozens of cars were seen submerged on waterlogged streets.
National rescue agency spokesman Yusuf Latif said the floods were triggered by extreme downpours.
"The rainfall intensity is very high due to extreme weather in Jakarta and it's been raining since yesterday night," Latif told AFP.
"Our top priority is children as well as infants and the elderly."
No casualties have been reported so far, he added.
Jakarta, a megalopolis that is home to around 30 million people, is frequently hit by floods in the rainy season.
The city saw some of its deadliest flooding in years in January last year after downpours that also triggered landslides.
At least 67 people in Jakarta and nearby cities were killed in that disaster, with the floodwaters reaching the second floor of some buildings after rivers burst their banks.
Meanwhile, the Jakarta Post reports, heavy rains in the capital city and surrounding areas from Friday to Saturday triggered floods that have deluged large parts of Greater Jakarta and disrupted the transportation system across the capital.
The flooding forced thousands of Jakartans to take to shelters and it is not expected to recede soon as the weather agency has forecast that the extreme weather conditions are expected to continue for the next several days.
The Jakarta Disaster Mitigation Agency recorded nearly 200 neighborhood units (RT) across the capital inundated by floodwater as of Saturday morning with 1,361 people forced to take shelter away from their homes.
The flooding ranged from around 0.4 to 2.5 meters in depth, with East and South Jakarta the hardest-hit areas.
According to the provincial administration flood monitoring website pantaubanjir.jakarta.go.id, Cipinang Melayu subdistrict in Makasar district, East Jakarta, was among the worst hit areas as the floodwater reached depths of 2.5 m.
State-owned electricity firm PLN cut off electricity in several areas of Jakarta and West Java that were affected by the floods. PLN Java, Madura and Bali business director Haryanto said in a statement that the electricity firm had deployed 6,170 personnel to restore electricity in the affected areas.
Traffic disrupted The flood also disrupted the city’s transportation system as it inundated several arterial and toll roads in Greater Jakarta.
The Jakarta Police’s Traffic Management Center reported that several arterial roads were inundated by floodwater, including Jl. Kapten Tendean, Jl. Kemang Raya and Jl. Jenderal Sudirman. Kompas.com reported that several parts of Jl. Sudirman were still inundated as of late Saturday evening.
Toll road operator PT Jasa Marga reported that several sections of the Jakarta-Cikampek, Jakarta-Tangerang, Jagorawi, the inner-city and outer ring road toll roads were impassable on Saturday due to the flooding.
The operator applied a contraflow traffic system on the Jakarta-Cikampek toll road to alleviate traffic congestion.