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, the meteorological agency said.
A nine-year old girl killed by a falling wall at her school was one of three confirmed fatalities.
An elderly man was also killed by a collapsing wall while another was trapped below a bookcase at home, national broadcaster NHK reported.
Several people were trapped in elevators and roads were cracked with broken pipes spilling water.
Some 170,000 houses were left without power and gas supplies to more than 100,000 homes were stopped, the Japan Times reported.
The earthquake registered as 6.1 on the country’s scale, a level at which it is difficult to remain standing.
Both the high-speed Shinkansen and local trains suspended operations during the morning commuting hours.
The quake also affected the cities of Kyoto, Nara, Hyogo, and Shiga.
The meteorological agency warned the quake might be followed by another big tremor in the coming days.
There are also warnings that rain and landslides will continue to pose a danger for several days.
The quake also hit several key industrial areas near Osaka with companies like Panasonic and Daihatsu saying they were suspending production at their affected sites.