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.
An elderly man was also killed by a collapsing wall while another was trapped below a bookcase at home, national broadcaster NHK reported.
'I thought my time was up'
Atsushi Yokoi, a research scientist who lives in Ibaraki-shi near the epicentre of the tremor, told the BBC he was asleep when the quake struck.
"The earthquake woke me up," he said. "It felt like strong sideways shaking and lasted about five seconds, and I stayed there until it stopped."
After sending messages to his family and friends, he went to work to check the damage to his research equipment.
"Though most public transport was still paralysed, buses were working. All the experiments planned have been cancelled and postponed until we are absolutely sure that there's no risk of an aftershock."
Ibaraki-shi resident Gloria Randriamihaja was also woken by the earthquake.
"It only lasted a minute but it seemed so long. My apartment was messed up, broken glasses on the floor, fridge open.
"The whole building was shaking, I was so scared, telling myself 'Gloria this is it, your time is up.' Finally the [shaking] stopped," she told the BBC.