The Irishman bagged his sixth league goal of the season as the Cod Army battled from behind to stun promotion-chasing Rovers.
Jason Lokilo had rifled the visitors ahead with his first professional goal after just eight minutes.
However, a spirited fightback from Town ended the visitors’ five-game unbeaten run and saw the home side claim three points at Highbury for the first time since November.
Rotherham United loanee Kyle Vassell equalised for Simon Grayson’s side on the hour mark before Madden and Danny Andrew secured victory.
Grayson made one change to his side with Charlie Mulgrew recalled to the starting line-up and Josh Morris dropping to the bench.
Rovers’ boss Darren Moore made three changes with Scott Robertson, Lokilo and John Bostock all handed starting roles at the expense of Madger Gomes, Jon Taylor and Taylor Richards.
It was Rovers who had the perfect start when Matt Smith picked out Lokilo and he beat Alex Cairns at his near post.
The visitors then suffered a blow when captain Tom Anderson was forced off after only 14 minutes with a head injury, having been clattered in a goalmouth scramble.
Andrew lashed a shot just wide, though at the other end, Brad Halliday tried his luck for Rovers but his effort flew well off target.
Town’s Callum Camps smashed an ambitious long-range drive wide before the home side were nearly caught on the counter-attack.
Mulgrew carelessly gave the ball away but Cameron John shot wide from an acute angle.
Andrew had a powerful shot charged down and Mulgrew went close from 35 yards as Fleetwood forced the pace.
Dan Batty forced a good low save from Ellery Balcombe, who also thwarted Vassell with a fine point-blank block three minutes before the break.
Rovers were denied a second goal a minute before half-time when Cairns palmed away Joe Wright’s close-range header.
Balcombe gathered a Madden effort 70 seconds after the restart but Town’s pressure eventually paid off when Vassell turned brilliantly on the edge of the box and rifled an effort into the bottom right corner.
It got even better for Grayson’s charges as Madden completed a fine turnaround with a cool finish.
Balcombe was sold short by Gomes’ backpass and Madden beat him to the ball before slotting home to turn an absorbing contest on its head.
For good measure, his first goal for nearly a month saw him leapfrog David Ball to 42 league goals for the club.
Fejiri Okenabirhie headed inches wide and John was thwarted by a superb reaction save from Cairns late on.
Andrew then ensured victory with a stunning strike as the Cod Army registered their first home league win since beating Plymouth Argyle on November 21.
Fleetwood Town: Cairns, Andrew, Connolly, Camps, Mulgrew, Rossiter (Finley 69), Madden, Vassell (Saunders 88), Donacien, Batty, Holgate. Subs not used: Coleman, Duffy, J Morris, McKay, S Morris.
Doncaster Rovers: Balcombe, Halliday, James, Anderson (Wright 14), Robertson (Gomes 61), Okenabirhie, Lokilo (Bogle 74), Smith (Taylor 74), Bostock (Richards 61), Butler, John. Subs not used: Jones, Simoes.
Referee: Andy Haines.
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