The left-hander will be 35 next season and becomes a free agent.
The decision Friday completes a $137.5 million, six-year contract that was agreed to before the 2008 season.
Santana was a two-time Cy Young Award winner with Minnesota. But he went 46-34 with a 3.18 ERA during the term of the deal, missing the 2011 and 2013 seasons following shoulder surgery. In 2012, he pitched the first no-hitter in Mets history.
He has a 139-78 record with a 3.20 ERA in 12 big seasons.
Source: Associated Press