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He made the announcement at the grand opening of Salesforce Tower.
The philanthropic arm of the company will donate $1.5 million to the initiative, which will be matched by Benioff and his wife Lynne.
WATCH: San Francisco's Salesforce Tower now tallest in city
VIDEO: SF's Salesforce Tower now tallest building in city
The money is being raised for the Heading Home Initiative, a joint effort conceived by late San Francisco Mayor Ed Lee and the City and County of San Francisco along with the San Francisco Unified School District, private philanthropy and Hamilton Families.
"Homelessness is the most urgent issue we face in San Francisco and it is unacceptable for any child to sleep on the street," Benioff said in a statement. "As a city and community, we have a moral obligation to make sure that every person and family in our city has a home. Lynne and I are proud to support the tremendous work of Hamilton Families and the Heading Home Initiative to end family homelessness."
WATCH: Topping off ceremony held for Salesforce Tower in San Francisco
Topping off ceremony to be held for Salesforce Tower in SF