Nikitin, 26, registered seven goals and 25 assists for 32 points with 18 penalty minutes in 61 games with the Blue Jackets and St. Louis Blues in 2011-12.
He was acquired by Columbus from St. Louis in exchange for Kris Russell on November 11, 2011.
"We were very pleased with the way Nikita played after joining us last season as he became a significant contributor on our blue line," said Blue Jackets GM Scott Howson. "He made tremendous strides this year and will continue to be an important part of what we believe is a very good group of defensemen."
St. Louis' fifth pick, 136th overall, in the 2004 Draft, Nikitin has collected eight goals and 33 assists for 41 points, and 28 penalty minutes, in 102 career NHL games.