Authorities were notified at around 4:30am Thursday that Ms Papini had been located on a rural road in the YOLO County. She was found by a passing motorist and was bound with restraints.
Police are now searching for two women driving a dark colored SUV who are believed to be armed with a handgun.
"We will not rest until Sherri's captor or captors are identified and brought to justice," said Sheriff Tom Bosenko, adding that the community should remain cautious.
There had been a reward for Ms Papini's safe return, but police have not confirmed whether or not the ransom was paid.
Investigations into what exactly occurred during the three weeks since her disappearance are ongoing.
The disappearance came soon after three women were murdered, in separate incidents, while jogging in the US, and fears were growing that Ms Papini had also been abducted.
Panini's sister had ruled out the possibility that the mother of two had simply left. “She was out for a run. She wouldn’t leave her babies,” Sheila Koester told The Toronto Sun.
Her husband had been appealing to the public for help, telling KRCTV: “Bring her home, bring her home, just bring her home. Bring her home safe there is a $50,000 reward just bring her home.”
"If she is listening I want to say, 'We are trying, we are trying the best we can and I am sorry I'm not there,'" said husband Keith, crying. "I'm coming honey. I am trying, I'm doing everything I can and I love you.”
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