The USGS says it was about three miles from the San Francisco Zoo near the San Andreas Fault and the depth of the quake was five miles.
There were no immediate reports of damage or injuries, according to the San Francisco Fire Department.
The quake was mainly felt in San Francisco and on the Peninsula, but the USGS says it was felt as far north as Marin County and as far south as San Jose.
A first aftershock came in at 2.5 magnitude at 9:39 a.m. and a second 3.0 magnitude aftershock hit at 10:48 a.m. Both are in the same location as the original quake.
Just before sunrise Friday morning, Max Gardiner was in the process of getting up to start his day when he noticed some unexpected shaking.
"I was just puttering around and making coffee and I noticed like the things in the kitchen started shaking, like the glasses in the cabinets so I kind of froze," Gardiner said.
Robin Darrah, an overnight guard at the San Francisco Zoo, explains what he felt.
"I felt a little wobbliness in my legs for a moment like I was getting really tired and for a second there, it was like wow the grave shift really got to me tonight you know?" Darrah said. "And then I heard one of my gates make a little rattle sound, I was like ok so I go to look at it and right when I turn the corner, I hear a call on the radio saying, hey did you feel the earthquake?"
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For this earthquake, no one got an early warning on the MyShake app.
"This is lower than a magnitude four earthquake and that is the main reason why no one received a shake alert powered on their phones, because it was too small," Robert de Groot, a USGS scientist said.
Groot explains earthquakes of these size happen more often than we think. California has around 50 a day.
Still, they want to use this a reminder to stay prepared.
Prepare NorCal: Disaster Preparedness Resources
"Basically we tell people probably not something bigger from this particular event but still be ready for earthquakes that can happen in other places," he said.
Because of the small size, no tsunami alert was triggered like San Francisco experienced in December.
The USGS also wants to remind people if they feel an earthquake again, to drop, cover and hold on.