Nicky Ajose’s goal in the final minute has given Exeter a 1-0 half-time lead over the Blues at half-time in the Leasing.com Trophy.
Teddy Bishop and Freddie Sears both made their first starts of the season playing off lone central striker Will Keane with Cole Skuse and Andre Dozzell in the centre of the midfield.
Toto Nsiala, James Wilson and Luke Woolfenden - two of only three players who started at Wycombe on Wednesday to keep their places - were the back three with Myles Kenlock and Gwion Edwards - the other - the wing-backs. Tomas Holy was back in goal.
Exeter made 10 changes from the team which won 1-0 at Forest Green Rovers on New Year’s Day with former Blues midfielder Lee Martin on the bench.
The Grecians were forced into a late change of keeper after Lewis Ward picked up an injury in the warm-up. Sub Jonny Maxsted started with youngster Jack Arthur on the bench.
Town began the game on top with Bishop making a couple of early trademark pacy dribbles towards the Exeter penalty area, despite a surface more Sunday league than EFL.
But the game’s first shot came in the 10th minute - with Grecians fans still streaming into the ground - when Joel Randell cut inside Edwards on the left of the box and hit a low shot which Holy claimed at the second attempt.
On 12 Ajose looped an effort well over after being found in space on the left, then at the other end Bishop almost found himself in on goal after the ball dropped for him on the edge of the area but his touch let him down and Alex Hartridge stabbed away from him. Two minutes later home skipper Jake Taylor shot over from distance.
Nsiala headed Town’s first attempt at goal into the side-netting from a tight angle from a Dozzell ball in from the right following a corner.
Taylor curled over for the Grecians, who were having a lot of the ball and plenty of shots from distance but without testing Holy.
Most of the game had been played in the Town half but on 36 Skuse looked the break on halfway but was tripped by Matt Jay, who was shown the game’s first yellow card by referee Josh Smith.
As the half moved into its final five minutes the Blues began to put the Grecians under pressure and on 40 went very close to going in front. Keane got round his man on the right, cut the ball back, hit a defender and struck the post before bouncing away from goal.
Town kept the ball around the Exeter box and eventually it was played out to Dozzell, whose shot from 20 yards was going wide to the left of goal until Keane nodded it not too far past the other post. A minute later, Keane was yellow-carded for frustratedly kicking the ball away.
However, in the final minute of the half, the home side took the lead. Nigel Atangana sent a ball in from the right which was flicked on to Ajose at the far post from where he struck a shot off the inside of the woodwork and over the line.
Moments later, referee Smith ended a rather understated half in which the Blues had struggled to make their divisional superiority tell on a pitch which was hardly conducive to playing passing football.
Until the brief spell when the Exeter post was hit and Keane nodded just wide, Town had rarely threatened other than when Bishop, who had had a lively half, had made breaks forward.
The home side had seen more of the ball but until their goal had been limited to efforts from distance which had failed to trouble Holy.
Town: Holy, Woolfenden, Nsiala, Wilson, Edwards, Skuse (c), Dozzell, Kenlock, Bishop, Sears, Keane. Subs: Norris, Jackson, Norwood, Judge, El Mizouni, Garbutt, Dobra.
Exeter: Maxted, Dyer, Warren, Hartridge, Richardson, Taylor (c), Atangana, Jay, Randall, Ajose, Seymour. Subs: Arthur, Martin, Bowman, Collins, Kite, Chrisene, Dean. Referee: Josh Smith (Bedford). Att: 2,299 (Town: 420).