The incident reportedly started as a hit-and-run and may also be connected to the abduction of a man in Chula Vista according to San Diego Police Chief David Nisleit.
Media reports said the shooter was a woman who had fired from an upper floor of a parking garage.
"As officers were responding, one officer fired two rounds at the suspect, but did not hit her", Nisleit added.
Police responded to reports of an active shooter at City Hall Parkade around 11:00am PT, about three blocks away from the end of the famed marathon. Police didn't immediately say if there were any injuries.
Spectators described on Twitter hearing at least one shot fired near the finish line of the 2018 Rock "n" Roll Marathon.
The race was halted for about 10 minutes and rerouted, marathon officials said.
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"She had a gun in her hand most of the time during this incident", he said.
"There's no longer a threat to the community", the San Diego Police Department tweeted.
The local Fox outlet said the firing had frightened scores of runners near the finishing line as the marathon was winding down.
Police first received calls about an active shooter around 10.51am (1751 GMT). He said it started when a police sergeant working the marathon was flagged down by the victim of a hit-and-run, who pointed out the auto being driven by Williams.
A woman with an airsoft gun was taken into custody almost an hour after the first reports of shots and a San Diego police officer was hospitalized with what has been described as a self-inflicted wound. "It was like police, police, police, siren, siren, siren". The shooting had just occurred in the parking garage they were headed to the nearby theater. They were later escorted into the theater with the others, who shuffled past the yellow police tape.
The 26.2-mile (42.2-kilometer) marathon course weaves its way through the city and also includes a half-marathon and a 5K run. More than 25,000 runners were expected to participate.