Boll, 26, will earn $950,000 in 2012-13 and $1.15 million in 2013-14.
Boll had two goals and an assist with 126 penalty minutes in 54 games with the Blue Jackets in 2011-12. He ranked second among on the club and 15th in the NHL in penalty minutes. In 2010-11, he went 7-5-12 and 182 penalty minutes in 73 games.
"Jared is a hard-working, honest player who gives everything he has every time he steps on the ice," Columbus general manager Scott Howson said. "He has also been a great ambassador in our community and we are happy that he will continue to be a Blue Jacket."
Boll was Columbus' fourth pick (No. 101) in the 2005 Entry Draft. Overall, he is 22-24-46 with 863 penalty minutes in 345 NHL games.
The Blue Jackets also signed defenseman Nick Holden to a one-year, two-way deal Saturday. Holden will earn $550,000 at the NHL level and $105,000 at the AHL level.
Holden, 26, had three goals, six assists and 14 penalty minutes in 25 games for AHL Springfield in 2011-12. He missed the majority of the season due to injury.