The tremor measured 5.1 on the Richter scale, according to the Athens Institute of Geodynamics, but the US Geological Survey gave it a preliminary magnitude of 5.3.
The quake was "strong but fortunately not very long," according to one witness quoted by the European Earthquake Monitor.
There was no immediate word on injuries or damages.
Witnesses said people were gathering on the streets, after the quake, which was caught live in the studios of state broadcaster ERT.
The quake sparked limited power cuts around the city and the fire brigade reported receiving calls about people being trapped in elevators.
Venetia Rainey, a journalist based in Athens, said she initially thought the tremor was construction.
“I noticed the flat vibrating slightly but thought it was just the building works outside," she said.
"Then after 10 seconds the whole building moved and the walls shook from side to side for about 10 seconds again."
"I ran to the balcony to see and saw lots of people in the street on their phones, a car alarm was going off."
In 1999, a 6.0 magnitude earthquake struck the Greek capital, killing at least 143 people and causing over 100 buildings to collapse.