The 34-year-old had not made a first-team appearance for the Grecians since November.
Exeter boss Paul Tisdale told the club's official website: "He made a huge contribution for us last year and put in some really good performances. Especially away from home he put in some terrific performances.
"He was a really instinctive player with real courage on the ball, and a tough-tackling player. I really enjoyed seeing him play for us."
Doherty played 45 times for Exeter after joining the Devon side from Bath City in July 2012.