The quake was reported at 4:10 p.m. in an area just south of Mt. Hamilton and 13 miles east-southeast of San Jose City Hall, according to the USGS.
The tremor had a depth of 4.4 miles, the USGS said. People in the East Bay and San Francisco reported feeling the quake.
BART briefly shut down service to check for damage from the temblor, but was back up and running within five or 10 minutes, a dispatcher said.
An employee at the Reid-Hillview Airport, the closest airport to the quake's epicenter, said operations were continuing as usual there.
"We felt it, but as far as we can tell, nothing fell down, and no aircraft were damaged or buildings were damaged," he said.
The owner of Ornamental Edibles, which sells vegetable seeds out of San Jose, felt it 5810 Killarney Circle.
"There was a little precursor, a little bit of a shake and then a jolt," store owner Pam Wiggitt said, adding that nothing was damaged and business wasn't interrupted.
"By the time we looked at each other it was almost over," said Margie King, owner of MK Technical Services, a staffing agency at 4349 San Felipe Road in San Jose.
San Francisco residents also felt the quake.
"My cubicle was swaying and it took me a minute to realize it was not me or anyone walking by," said Pamela Ringer-Britz, a project manager at SFL Data at 100 California St.
"Everyone in my office felt it," she said.
A few aftershocks have been reported in the same location, including one with a preliminary magnitude of 2.6, according to the USGS.
"The direction of the fault motion was more or less ideal for everyone to feel it," said seismologist Walter Mooney, Ph.D.
Moments after 4:10 p.m. when the quake struck, viewers started calling the ABC7 newsroom and posting messages on out Twitter and Facebook pages.
One person wrote, "Yes, we rocked and rolled in the Hayward hills." Alex posted, "I live in Santa Clara and the house was moving side to side." Andrew wrote, "On floor 22 in SF... It rocked a bit ... I'd imagine down in SJ they really felt it." Then, Laura then responded with "Totally! My building rocked and shook in downtown San Jose." In parts of the East Bay residents also reacted.
The last large one along the Calaveras fault - which is where today's quake was centered - was in 1984. The 6.2 quake hit Morgan Hill hard.
Seismologist call today's quake - a light one that happens about once a year. And the reason it really rocked the East Bay is because the quake literally pushed in that direction.
"It was a sliding earthquake and the push to the north that everyone felt emanated from this point and was clearly felt throughout the Bay Area," said Mooney.
Mooney said a 4.1 quake is too small to cause any damage.
ABC7 did not receive any reports of damage or injury as a result of today's quake.
ABC7's Lisa Amin Gulezian contributed to this report
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