The 33-year-old Northern Ireland international has been a key part of Paul Tisdale's squad at St James Park since signing a six-month deal in the summer.
And the former Bristol City man, who has added some steel to the Grecians' midfield, has made 11 starts and six substitute appearances in the opening five months of the League Two season.
"I've been very happy with Tommy," Tisdale told BBC South West. "He's obviously happy with us, he's enjoying his football and I'm pleased.
"He's a proper competitor, he's a very good footballer, got a very instinctive football mind and can see the situation in front of him very quickly, better than most. I didn't want to weaken the side by Tommy leaving us."
Doherty, who has often played alongside another experienced midfielder in Matt Oakley, had been playing non-league football with Newport and Bath after spells with Wycombe and Bradford before joining up with the Grecians.