The vote was 28-1. In addition to Yee, who represents a San Francisco district, it would affect two Los Angeles-area senators, Ronald Calderon, who is under indictment, and Roderick Wright, who was convicted in January of voter fraud and perjury.
All three are Democrats. The party now holds 28 senate seats to 11 Republicans and one independent.
Senate President Pro Tem Darrell Steinberg said he plans to introduce a constitutional amendment that would allow the legislature to vote to suspend members without pay. Under current law, Yee, Calderon and Wright would continue to be paid.
Yee, who has served in the assembly and senate for a decade, was arrested Wednesday and released on $500,000 bond. The senator, a longtime gun control advocate, faces charges that include being involved in gun trafficking.
Others arrested after a four-year FBI investigation include a former president of the San Francisco school board and Raymond "Shrimp Boy" Chow, a Chinatown gangster who had become a counselor to at-risk young people after being released from prison 10 years ago.