Lincoln got back on the winning trail thanks to a cracking second-half goal from Scott Willis.
The midfielder, signed in the summer from non-league football, fired a 25-yard shot straight into the top corner leaving Exeter keeper Kevin Miller rooted to the spot.
The 75th minute goal was enough to confirm Lincoln's second-half domination and give the Red Imps their fifth home win of the season.
Lincoln started well with Willis creating an excellent 12th minute chance for Adie Mike but the striker's diving header was well saved by Miller.
Exeter mounted their first attack in the 19th minute with former Lincoln man Justin Walker firing in a low shot which struck the post and then spun in front of the empty net with Lincoln keeper Alan Marriott stranded.
Simon Yeo wasted three good first-half chances and Lincoln almost paid the penalty early in the second half when Exeter's Kwame Ampadu was put clear but blasted his shot wide.
Lincoln's Ben Futcher headed against the crossbar but the game turned in the 66th minute when Yeo was fouled by Neil Whitworth as he raced into the box.
Whitworth was shown the red card by referee Eddie Evans and from then on Lincoln were on top.
Despite the result Exeter's new head coach Neil McNab was pleased with the effort his players put in.
"I can't criticise them for their work rate," he said. "They kept battling after we were down to ten men and there were a lot of plusses to come out of the game.
"I thought Steve Flack played very well up front and the only mistake he made was when he missed a late chance."