Fleetwood forward Ched Evans was sent off for violent conduct on Bristol's Tom Lockyer when the score was locked at 1-1.
But despite a valiant defensive performance when down to 10 Town could not hold on with James Clarke popping up at the death.
It was an end-to-end start at Bristol Rovers.
Fleetwood nearly struck within the first minute.
Ched Evans threaded the ball to Hunter in space on the left of the box but he could only fire straight at Jack Bonham.
It was a chance you would have expected him to score and Town were nearly punished for that missed opportunity moments later.
Alex Jakubiak only had a brief spell at Fleetwood Town in the 2016-17 but managed to carve his name in the history books having been the 100th player to feature for the club in the Football League.
The forward was instrumental in creating a chance for Ed Upson but his effort was blocked by Nathan Sheron.
Jakubiak then had a chance of his own and was left kicking himself after he blasted over.
The forward found himself in space in the box but failed to test former team mate Alex Cairns.
Up the other end Hunter curled an effort wide of the right stick but he was just getting his eye in for later in the game.
The chances dried up for Town but Bristol kept testing Cairns.
The in-form shot-stopper handled everything Rovers threw at him but it was just for the grace of god that he did not concede in the 21st minute.
Reilly's left footed volley crashed into the post and then rebounded to the unmarked Rodman but he could only divert the ball wide with the goal gaping.
Town went on to punish the hosts for that miss.
McAleny's vision saw him pick out Madden and the forward drove Town on.
He held the ball up and slid it to Hunter in space on the left with the winger whipping the ball into the bottom corner from outside the box in the 28th minute,
It was an effort for his scrapbook with Evans blasting a set-piece straight at Bonham minutes later.
While they looked sharp on the attack Fleetwood's defending was far from picture perfect as the half wore on.
After Madden had cleared Tareiq Holmes-Dennis' initial corner from the left Town were felled at the second attempt.
Holmes-Dennis was the provider once again with Rodman flicking the ball on at the near post.
Reilly was the quickest to react as he nodded the ball past Cairns.
It was a deserved goal for the managerless side with Fleetwood looking shaky at the back at times.
Fleetwood found themselves up against it just 10 minutes into the second half though as referee Brett Huxtable took centre stage.
Evans had already been booked in the first half but when he went down injured after a tangle with Tom Lockyer and with the home faithful screaming for him to be sent to the stands the referee brandished a straight red.
To say it was a far from impressive game from Huxtable is an understatement.
The referee looked to have got that Evans decision wrong and managed to miss a number of fouls throughout the game.
The referee has spent the majority of the term in League Two, this only the official's fifth League One game of the season and it showed.
Barton was forced to make changes sending on Biggins for McAleny and later Morgan for Holt.
Rovers asked questions of Town as the half wore on but the defence made up for a shaky first half with a valiant and heroic display in the second half.
Town's 10-men made numerous blocks and clearances to thwart Rovers with Coyle nearly giving Fleetwood the lead.
Hunter and Ross Wallace combined well on the left before finding Coyle in acres of space outside the box.
His effort took a wicked deflection that flew just wide of the right stick.
But Town were forced to defend again in the final 12 minutes though with Morgan on for extra defensive cover they handled everything the hosts could muster.
But that was until the fourth official signalled six minutes added time with Rovers then throwing everything but the kitchen sink at Fleetwood.
Substitute Chris Lines hit the cross bar before James Clarke also sent the ball crashing into the woodwork.
Matthews fired wide and Fleetwood looked to have escaped.
But that was until Lines, who was booked for a push on Ross Wallace, whipped in a free-kick from the right that Clarke eventually blasted home in the 94th minute.
Fleetwood: Cairns, Coyle, Sheron, Eastham, R Wallace, McAleny (Biggins 58), Marney, Holt (Morgan, 65), Hunter (Taylor, 85), Evans, Madden. Subs: P Jones, Rydel, Hill, Garner.Bristol Rovers: Bonham, Holmes-Dennis (Matthews, 75), Lockyer, Craig, Upson, O Clarke, J Clarke, Jakubiak, Reilly, Kelly, Rodman. Subs: Smith, Payne, Nichols, Lines, Broadbent, Partington, Matthews.
Attendance: 7159 (68)