Ten people were taken to hospital suffering from light injuries caused by falling debris.
Some buildings were damaged in what was the strongest in dozens of tremors since Etna erupted on Monday.
Volcanic ash had earlier covered nearby villages and Catania airport had to temporarily suspend operations.
The earthquake struck at 03:19 local time (02:19 GMT) on Wednesday near the municipality of Viagrande.
In the village of Fleri, an 80-year-old man had to be rescued from his home. A local church was also damaged.
Italian media reported panic among residents, many of whom ran out into the streets. People on the mountainside were told to escape quickly.
There were also reports of buildings shaking in Catania, a city of more than 300,000 people.