"Five people died, three from East Jakarta and two from Bekasi," said Firman Hairuyusuf, an official at Indonesia's natural disaster centre on Saturday, referring to a town east of the capital.
"The worst hit area is Bekasi. In Jakarta the waters have started to recede."
The floods affected both slums and up-market areas in Jakarta, a low-lying city built originally on swampland.
The floods have caused major power outages and telephone lines were also down in some parts of the city of 9 million as flooding affected underground cables, officials said.
Soldiers were also drafted in to help evacuate residents in some areas.
Scores of the city buses that many residents rely on were stranded in traffic jams or due to lack of fuel on Friday.
Endro Santoso, an official at the Meteorology agency, told the Jakarta Post that the city could suffer another week of heavy rains.