Airports in the area were closed for several hours, train lines interrupted and factories had to halt production.
The 6.1 magnitude quake did not trigger a tsunami warning and nuclear plants in the area are operating normally.
Japan lies in a particularly earthquake-prone region and accounts for around 20% of quakes worldwide of magnitude 6.0 or more.
Monday's quake in Osaka occurred just before 08:00 local time (23:00 GMT Sunday) north of the city.
A nine-year old girl killed by a falling wall at her school was one of three confirmed fatalities.