The US city is facing a housing crisis, exacerbated by landlords renting out their property to visiting tourists rather than residents.
Under the rejected Proposition F, landlords would have been fined if they rented out their homes short-term for more than 75 days a year.
The result of the poll was closer than anticipated.
AirBnB lets landlords advertise property for short-term rentals, often undercutting hotels.
Proposition F would have seriously affected its operations in San Francisco, so the company spent $8m (Â£5.2m) on a "No on Prop F" campaign.
The "Yes" campaign, which lost by about 13,500 votes had just $1m (Â£650,000) funding.
Proposition F has been defeated, but despite the huge amount of money invested by AirBnB, the result was still pretty tight.
In fact, the result was closer than the "Yes" camp had imagined.
Dale Carlson, the "Yes" spokesman, had expected to be "completely blown out" in the vote.
In the end, the No supporters only won with 55% of the vote, and that isn't by much.
Given that regulators here now plan to use different legislative methods to limit AirBnB in San Francisco, this result may actually play in their favour.
Read more: San Fran votes on â€˜AirBnB law'
San Francisco voters have rejected a proposal to limit short-term rentals offered by AirBnB and similar services.