Steve Tully's first goal for 16 months and Matt Taylor's fine header helped City to a fantastic away victory at Meadow Lane this afternoon.
After a forgettable first half Tully showed striker's instincts to open the scoring after O'Flynn's shot was well saved and City's skipper made the game safe when he towered above his marker to head Harley's delivery into the far corner.
Paul Tisdale made two changes from the team 'embarrassed' on Monday night, Steve Tully and Scott Golbourne returning for Liam Sercombe and Billy Jones.
It meant a return to the conventional 3-5-2 formation with O'Flynn and Jamie Cureton as the hard-working strike duo.
It took City 91 minutes to chalk up a shot on target against the Bees but just six this afternoon. David Noble's lofted ball found Cureton on the right hand side, he flew into the box and had a low effort saved by Nelson at his near post.
O'Flynn rolled a shot at Nelson and at the other end Jon Harley shot over but there was little to get excited about during a solid and very unspectacular first half.
In the final minute of the 45 Matt Taylor's header from Harley's corner landed on top of the net but that was that. There was plenty to be positive about though at the interval, City had rarely been troubled and the back and certainly were matching Ince's men.
The away side created the first chance of note in the second half when Troy rose to meet another Harley corner but his header hit the stanchion behind Nelson's goal.
Three vital blocks from James Dunne then kept the Notts attack at bay as the former Arsenal man put his body on the line for the cause.
City had flown out of the traps and made it count when an unlikely scorer found the bottom corner on 54 minutes. Harley's magic feet made space for himself in the left hand corner and from his pull back O'Flynn's shot was superbly saved. But the rebound fell kindly for City's number two to net a poacher's finish from 5 yards out to give Exeter the lead with only his second Grecian goal. His team-mates and manager joked afterwards about him shinning the ball home but they all count!
Penalty appeals were then waved away by the referee on 64 minutes when Troy tackled Lee Hughes inside the box. Then a minute later the former West Brom man saw yellow for a coming together with Duffy after Hamer had claimed a long ball.
On 67 minutes the 414 travelling faithful could have been celebrating again when Troy headed down Harley's delicious free kick but Cureton's right footed effort flew over the bar.
But Harley's next delivery was a vital one. He whipped in a corner from the left hand side, earned after a fantastic flowing move, and Matt Taylor leapt to head the ball into the far corner. A crucial second for the Grecians and surprisingly the captain's first of the campaign.
Dunne continued his fine display with a string of vital tackles and Cureton was almost in after a one-two with O'Flynn. Tully was then replaced by Liam Sercombe as City looked to play out the final six minutes.
A late scare was then avoided thanks to the right hand post that kept out Hughes' drive with a minute to go.
But that was as much as the home side could muster and City played out the dying minutes for three vital points.
City looked very comfortable back in their familiar 3-5-2 formation and the morale boost this victory has given them will hopefully stand the Grecians in good stead when Swindon come to The Park on Tuesday night. Tisdale's troops now sit seven points behind the Play Off places and seven ahead of the Robins who occupy the first place in the relegation zone.
From front to back City's XI can be delighted with their afternoon's work. The fact that Notts County didn't muster a shot on target says a lot about the performance of the back five and the solid Ben Hamer behind them.
But in our opinion City's star man was James Dunne. He showed tremendous energy and passion throughout and made a string of crucial tackles and blocks to drive City on to a memorable away victory.