The moderate quake occurred about 13 miles from Borrego Springs, a community in the eastern part of San Diego County, just after 1 am PT, according to the U.S. Geological Survey (USGS).
Residents in San Diego and parts of Los Angeles felt shaking, too, according to CNN affiliate KABC.
Fortunately, there were no reports of injuries or damage, San Diego Sheriff's Lt. Andrea Arreola told KABC.
After the initial earthquake, about a dozen small aftershocks hit the area, the strongest being a 3.8-magnitude quake.
The first earthquake, which happened near the San Jacinto fault
, one of the most historically active faults in region, had some people on social media asking whether this was a precursor to something much stronger
The earthquake probably won't trigger something more powerful, USGS scientist emeritus and seismologist Lucy Jones told CNN.
On Twitter, Jones shared a message stating the quake should not prompt alarm.
"We have never seen a San Andreas earthquake triggered by a San Jacinto earthquake. The 2 faults are 25 miles apart."
This means it is unlikely the earthquake would trigger something more powerful on another fault line because of their sheer distance from one another.
And the aftershock activity following the morning's earthquake are normal, she posted later on the social media site.
In March, geologist Julian C. Lozos discovered that the San Andreas and the San Jacinto faults may have ruptured together about 200 years ago
, creating an earthquake that was felt from north of Los Angeles to San Diego, based on historical data captured by missionaries in those areas.
In his report, he said it may be likely that this situation could happen again in the future.
"If there's a joint rupture it will create a larger earthquake, especially if it starts on the San Jacinto," Lozos told CNN back in March. "Say you're stressed out and you snap. You might then stress out your friend too. That's that same way faults work. They stress each other out."
But Friday's quake is not one of these scenarios, Jones said.
There's no doubt a massive earthquake is coming though, she added.
"The mountains are here and they are growing. However, we don't know when in a human lifespan that large earthquake will happen," she said.
The San Andreas fault is due for an epic tremor every 150 years, the USGS said
. It has been about 250 years since a powerful earthquake struck the region. An expeditionary force reported it in 1769 southeast of Los Angeles.
"We have twice the average recurrence time. This fault is storing a lot energy for a big earthquake," Jones said.
Although we don't know when to expect California's powerful quake, communities are starting to become more proactive about protecting their citizens and infrastructures from these natural disasters.
"Most people are afraid for dying in an earthquake, but we run the risk of ruining our economy if a big one hit. If there is no water or electricity people could not go to work," she said.
Government officials are slowly changing the way they approach earthquake safety, Jones said. Instead of being more reactionary to a disaster, community leaders are starting to plan to ahead.
"It used to be that people had to experience something in order to think it can happen to them," Jones said. "But our global society is changing the way we see earthquakes. Think about the earthquake in Japan which triggered a tsunami. Or Nepal. Or New Zealand. Or Haiti. We're able to see what's happening to other countries."