Sunderland and Portsmouth slip up to hand Luton and Barnsley automatic promotion
An excellent first half performance saw the Black Cats miss a number of chances to establish the kind of lead that would have kept their slender top-two hopes alive.
Fleetwood responded with a much superior showing after the break, Paddy Madden and Ashley Eastham scoring the crucial goals.
Sunderland now face a play-off campaign, though Portsmouth's home defeat to Peterborough United means they could still finish in third position.
They are two points behind Kenny Jackett's side with a superior goal difference.
Sunderland had started the game knowing a big win would be needed to keep their automatic promotion hopes alive and after adjusting to a surprise change in system from Fleetwood Town, they quickly began to establish control of the game.
Joey Barton had switched to a back three as he prepares for next season, former Black Cat Ross Wallace playing in an unfamiliar role at the base of central midfield.
That threw the Black Cats initially but with the home side visibly uncertain in their new shape, Luke O'Nien found there was plenty of space to attack down the right.
Max Power ought to have put his side ahead 12 minutes in when Lewis Morgan drifted into that space near the corner flag, cutting a good low cross into the centre of the box. Power arrived unmarked but fired straight at Alex Cairns, who was able to get down and save.
Another good move minutes later saw Lee Cattermole shoot from the edge of the area, his effort flying over the bar.
Sunderland were dominant and should have gone ahead when Lynden Gooch got in behind and teed up Will Grigg, who curled his shot off the woodwork with Cairns beaten.
Grigg then missed another good opening when he peeled off the centre-back to meet a chipped pass from Max Power, heading weakly at Cairns.
Fleetwood were offering little, their only threat coming as Bryan Oviedo failed to track his runner, wing-back Wes Burns advancing into space and playing in Ashley Nadesan, who drew a smart block from Jon McLaughlin.
The away side swiftly broke upfield and were ahead when Lewis Morgan whipped a delightful cross into the box, Cattermole rising unmarked to head home.
Barton's Fleetwood improved from there, though Morgan spurned a good chance when he fired wide from distance as Oviedo made a dangerous overlapping run.
The only frustration for Jack Ross at half time was that his side had not taken more of their chances, particularly with Portsmouth trailing at home to Peterborough United.
Barton unsurprisingly shuffled his pack at the break, and they began the second half with far greater intensity.
Though they failed to test McLaughlin with any effort of note, they pressed far more effectively and forced the Black Cats defence into a a number of aimless long balls out from the back.
The frontline was starved of service, Chris Maguire's weak effort from distance their only real effort on goal.
Ross shuffled his pack as they game entered the final quarter, Kazaiah Sterling and George Honeyman replacing Will Grigg and Chris Maguire.
Fleetwood had offered little in front of goal but levelled with fifteen minutes left on the clock, building a clever overlap on the right and crossing into the box, where Paddy Madden had the easiest of finishes.
They were inches away from a second moments later when Ashley Eastham headed a free-kick just wide of the far post, McLaughlin beaten.
That did spark something of a response from the Black Cats, who sprung a good counter when a clever ball from Cattermole released Sterling into space. Oviedo was set to connect with his ball across goal when Fleetwood were just able to clear the danger.
From the following corner James Husband looked to clear but sliced his clearance inches wide of his own near post.
The pressure continued and Morgan came close when a loose ball bounced to the edge of the area, his half volley flying over the bar.
Sunderland looked the more likely but last the game in the dying moments, Eastham rising at the back post to head home and condemn the Black Cats to their fourth league defeat of the season.
Sunderland XI: McLaughlin; O'Nien, Ozturk, Flanagan, Oviedo; Cattermole, Power; Gooch, Maguire (Honeyman, 69), Morgan; Grigg (Sterling, 65)
Subs: Ruiter, Matthews, Leadbitter, Hume, Dunne
Fleetwood Town XI: Cairns; Coyle, Eastham, Husband, Clarke (Sowerby, 45); Burns, Biggins, Wallace, Hunter; Nadesan, Madden
Subs: Jones, Southam-Hales, Baggley, Hill, Rydel, Mooney
Bookings: Burns, 70 Sowerby, 82 Hunter, 82 Wallace, 90