The floods were the most widespread to hit the city in recent memory. Authorities said at least four people were killed and 20,000 evacuated. Many more homes were flooded following five hours of heavy overnight rain that coursed through rivers already swollen by a long monsoon season.
Few areas in the city were spared, from wealthy suburbs to riverside slums.
Offices and schools were deserted and traffic ground to a halt. The international airport was operating normally, but travellers were finding it hard to get there.
"This is horrible," said Yanitha Damayanti, a bank teller stranded downtown. "For the first time in my life, downtown Jakarta has flooded."
The city has long been prone to floods, but successive governments have done little to mitigate the threat.