Paudie O’Connor’s header was not enough as City's unbeaten run came to an end in Devon.
The first chance of the match came in the second minute as Demtetri Mitchell broke down the left and fired the ball into the area, but his cross struck Sam Nombe and City cleared before giving away a free-kick in a crossing area. The resulting set-piece was taken by Joe White, but went straight out of play.
The Grecians went close to opening the scoring again in the 15th minute as Jay Stansfield was able to break through and cross, but Lewis Montsma diverted the delivery before Adam Jackson was quick to close down and block the follow-up.
In the 18th minute, Paudie O’Connor headed the Imps into the lead following the match’s first corner.
Gary Woods came off his line to punch clear, but mistimed his effort which allowed Regan Poole to head back across the area where O’Connor rose highest to nod his side ahead.
The hosts equalised in the 34th minute following a mix-up in the City backline where Nombe was able to pick up a loose ball and finish into an open net.
The Grecians looked to add another a few minutes after, as Nombe missed a one-on-one as he rushed beyond the City defence.
The striker had another chance in the following minute as Mitchell crossed into the box, but Nombe’s header was too high.
Just before half-time a City throw was headed on by O’Connor with the ball falling to Mandroiu, but the winger volleyed narrowly wide.
The hosts had a chance just after the break as White fired wide from just outside City’s box.
Exeter followed up with another chance in the 58th minute as they won a corner, but Alex Hartridge’s header went narrowly past the post.
The hosts kept pushing for another in the second half, but City did well to deny the Grecians on several occasions.
In the 70th minute Regan Poole won the ball just outside the hosts’ area and crossed to Diamond in the box but the forward couldn't quite get on the end of the delivery.
One minute later the hosts made their pressure count as Nombe scored his second for the day as he was able to break beyond City’s defence to slot into the bottom right corner.
In the 86th minute, Alex Hartridge was booked for the second time as he pulled Bishop down and was sent off.
The final action of the match saw the Imps nearly find the equaliser through a succession of corners, but the Grecians stood firm to see out their win.
Exeter: Gary Woods (Jamal Blackman 46’), Alex Hartridge, Rekeem Harper (James Scott 67’), Demetri Mitchell, Archie Collins, Jay Stansfield (Jonathan Grounds 86’), Sam Nombe (Jake Caprice 90+2’), Joe White (Kegs Chauke 67’), Josh Key, Will Aimson ©, Pierce Sweeney. Subs (not used): Jamal Blackman, Jack Sparkes, Josh Coley.
Goals: Nombe (34’, 73’).
City: Carl Rushworth, Regan Poole ©, Lewis Montsma, Adam Jackson, Ethan Erhahon, Paudie O’Connor, Ben House, Danny Mandroiu (Mide Shodipo 76’), Sean Roughan (Ted Bishop 67’), Matty Virtue (Lasse Sorensen 61’), Jack Diamond (Luke Plange 76’). Subs (not used): Jordan Wright, Max Sanders, Charles Vernam.
Goals: O’Connor (18’).
Attendance: 6,193 (284).
Referee: Sunny Gill.