The vote was six to one, with two abstaining. Richard Harmon cast the lone no vote.
Thomas cast the winning bid of $89,000 at an auction Jan. 22. The only other qualified bidder at the auction was Community First, a group which had been working with the city to purchase the building before the Council opted to proceed to auction.
The Council was to vote on approving the sale last week, but members raised questions about what their options were and wanted answers to concerns about whether the process had been fair.
Thomas plans to develop a community resource center with several programs, including child care, job training and performance arts. He is backed by an L.A.-based minister.