The quake was centered about 14 miles north-northwest of Borrego Springs and hit just after 1 a.m., according to the U.S. Geological Survey.
Residents reported feeling shaking from the earthquake in San Diego, West Los Angeles, Riverside and Woodland Hills.
SoCal residents miles away shaken awake by large temblor in San Diego County
There were no immediate reports of injuries or damage, San Diego Sheriff's Lt. Andrea Arreola said.
"At this point, we are just monitoring the area," she said.
Hemet police said the earthquake set off a lot of alarms at businesses.
The earthquake occurred along the San Jacinto Fault, historically the most active fault in Southern California, according to seismologist Lucy Jones. She added the quake was near the location of a magnitude-6.0 quake in 1937 and a 5.3-magnitude one in 1980.
Every EQ has a 5% chance of triggering an "aftershock" that is bigger than itself - always within a few miles of location of 1st EQ— Dr. Lucy Jones (@DrLucyJones) June 10, 2016
Within an hour, there were six aftershocks in the same general area, the strongest a magnitude-3.5 shaker at 1:06 a.m. with roughly the same epicenter but at a depth of 6.7 miles.
Another 3.5-magnitude aftershock struck a few hours later just before 4:15 a.m. about 15 miles north, northwest of Borrego Springs, according to USGS.
City News Service contributed to this report.