A tsunami warning after the quake, recorded by US monitors as being magnitude 6.9, was later cancelled.
The quake struck at a depth of 52.8km (33 miles) at 19:03 (12:03 GMT).
Indonesia has a history of devastating earthquakes and tsunamis with more than 2,000 killed last September on the island of Sulawesi.
The Indian Ocean tsunami of 2004 killed 170,000 people on the Indonesian island of Sumatra after a quake of magnitude 9.1.
"The chandelier in my apartment was shaking and I just ran from the 19th floor," Jakarta resident Elisa, 50, told AFP news agency.
"Everybody else ran too. It was a really strong jolt and I was very scared."
Another Jakarta resident, Rosa Erta, told Reuters news agency: "It was so strong, the lights and clothes hangers were rocking. I felt it strong. I was so scared, I ran down the stairs."
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