However, authorities warned of more rain and disruptions in the city of about 10 million people after Thursday's floods killed six people and turned Jakarta's main thoroughfare into a stream of red mud.
Other main roads were still full of water and choked with traffic on Friday as commuters struggled to return to work and emergency workers tried to clear the mess.
"Many roads will remain flooded for the next two or three days," police spokesman Boy Rafli Amar said. "Jakarta experienced quite a severe impact because 13 rivers flow into it from the south and west."
Large areas of the city were still without electricity after state utility PLN cut power in some places to avoid the risk of electrocution.
Investors however shrugged off the disruption, pushing the Jakarta stock index .JKSE up 1 percent to a record high.
The central bank said it saw the weather causing disruption to food distribution, which was likely to push up inflation this month. Torrential rain across the main island of Java has not damaged key crops such as rice and palm oil, officials said.
The state palace was inundated and a $700,000 Rolls-Royce was among scores of cars swallowed by the floodwaters on Thursday, witnesses said. Many businesses remained closed.
Soldiers using an excavator struggled to stem the flow after a large section of a canal burst, sending a torrent of dirty water into the heart of the capital. Debris including sofas and dead fish littered the soggy streets and police captured a 3-metre python in the city, wrestling it into a van.
Many parts of Indonesia are regularly inundated during the annual rainy season, bringing already strained transport systems to a halt, although this flood was the worst the capital had suffered since 2007. Jakarta mayor Joko Widowo has declared a 10-day state of emergency.
Widodo, elected last year, is under pressure to improve drainage to prevent regular flooding in the low-lying capital, and to fix Jakarta's notoriously bad traffic. Plans are under way for new toll roads, bus lanes and a metro system. (Additional reporting by Rieka Rahadiana, Janeman Latul and Adriana Nina Kusuma; Editing by Neil Chatterjee and Paul Tait)
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