A last gasp Cian Bolger header clinched a 1-0 win for Fleetwood and sent Uwe Rosler’s men up to fourth in the League One table.
Town left it late as Kyle Dempsey’s pin-point corner from the left was nodded in by giant defender Bolger in the 90th minute.
With Rochdale suffering a 4-0 home defeat to Oxford and Bradford drawing 1-1 with Millwall Bolger’s late effort saw Town climb two places up to fourth.
Rosler made four changes to the side that lost 1-0 to Championship side Bristol City in the FA Cup on Tuesday.
Rested trio David Ball, Ash Hunter and Bobby Grant returned to the starting line-up with George Glendon who was ineligible for the cup replay back in contention.
They came in for Chris Long and Devante Cole who moved to the bench with Jack Sowerby and Eggert Jonsson left out of the squad as Rosler named new signings Joe Maguire, Markus Schwabl and Wes Burns on the bench.
Fleetwood started brightly as Grant volleyed the ball way wide, Hunter fizzed the ball across goal after a well-worked counter that was orchestrated by Dempsey and then Grant got in around the back but his cross from the left was just nudged out of play by a Coventry toe.
It continued to be all Town as they dominated possession and fended off the hosts’ long balls up to Beavon and Thomas with Bolger commanding the back line and nodding everything away.
For once Glendon’s set-piece delivery was not up to his normal standard in the opening stages as Town wasted a number of corners and free-kicks.
Town always looked a danger on the counter and despite the worn pitch managed to string some good passing moves together but could not find that all important final touch or pass with Grant’s deflected effort from just outside the box skimming past the right post.
The game grew scrappy as Town failed to get the goal their early dominance deserved and nearly found themselves a goal down in fluke fashion just after the half hour mark. Coventry’s Andy Rose miss-hit his cross from the right and caught Cairns off his line but the keeper back-peddled and managed to just grab the ball and stop it going over the line.
Town nearly got their goal on the stroke of half-time as Glendon wriggled his way to the back line and put the ball on a plate for Ash Eastham but the defender just failed to connect in front of a gaping goal.
Fleetwood had an equally big chance just seconds into the second half as Bell raced down the left wing and cut the ball back for Hunter but his first time effort just fizzed past the right post.
Town were the better team but without a goal Coventry were not dead and buried as Callum Reilly’s header kissed the right post and half-time substitute Jodi Jones was just offside as he threatened to sprint one-on-one with Cairns.
Those chances woke the home crowd up but the game continued to be a scrappy affair.
Coventry had a big penalty shout waved away after Jones knocked the ball past Eastham in the box and dramatically tumbled to the ground but referee Darren Deadman waved away his claim.
Rosler gave new signing Schwabl his debut and Burns his second debut minutes later as Town searched for a winner.
But apart from a Bolger header that flew over the bar Fleetwood did not create any clear cut chances until the closing stages.
The lively Burns found himself in on the left after a fine looping ball by Schwabl but with the ball still bouncing his effort was just pushed round the post by Burge but Town finally got their goal from the subsequent set-piece.
Dempsey whipped the ball in from the left and onto the head of Bolger who hammered the ball home.
It could have been two moments later as Burns out-paced Coventry’s defence to sprint one-on-one with Burge but after drawing him out Burns’ low effort was just tipped away by the Coventry shot-stopper.
Fleetwood: Cairns, McLaughlin, Eastham, Bolger, Davies, Bell, Dempsey, Glendon (Schwabl, 69), Grant, Hunter (Long, 60), Ball (Burns, 75). Subs not used: Neal, Nirennold, Maguire, Cole.
Coventry: Burge, Willis, Turnbull, Rose (Lameiras, 85), Clarke, Reilly, Beavon (Jones, 46), Rawson, Haynes, Thomas, Stevenson. Subs not used: Charles-Cook, Reid, Gadzhev, Kelly-Evans, Harries.
Referee: Darren Deadman.