The vote came just hours after the Foreign Relations Committee approved his nomination by voice vote. Kerry has led the committee for the past four years.
The five-term Democratic Massachusetts senator was not expected to face real opposition from his colleagues.
Kerry was expected to submit his letter of resignation to the Senate Tuesday. He has served on the Foreign Relations panel for 28 years and led the committee for the past four.
The 69-year-old Kerry is a decorated Vietnam veteran and the 2004 Democratic presidential candidate. losing a close election to incumbent George W. Bush.
The Associated Press contributed to this report.