A jaw-dropping field-goal from Canberra Raiders five-eighth Aidan Sezer in the last 20 second of play ensured that Manly's turbulent season continued into Round 12.
Despite trailing by 12 points in the first half, the Raiders were able to pull off their fifth win of the season in traumatic fashion.
Nick Cotric got the home side pumping when he scored two tries in five minutes before assisting fullback Jack Wighton late in the game.
Wighton's try was converted by Jarrod Croker, levelling the score at 20-20 with three minutes left on the clock.
A chaotic final minutes of play followed before Sezer was able to boot the ball in between the sticks from out in front.
Manly was left devastated, blowing their chance at winning three on the trot when Trent Hodkinson missed a field-goal of his own.
They asserted their dominance on the game in the opening 20 when captain Daly Cherry-Evans and Joel Thompson both crossed over the chalk to lead 14-2.
But it wasn't enough to hold back the Raiders, who inspired by New South Wales bolter Cotric, were able to crawl their way back into the game.
His efforts earned him man-of-the-match honours with Manly fullback also having a blinder, running the ball for 149 metres in an outstanding performance.
Manly will head home to prepare for their match against the North Queensland Cowboys next week, while the Raiders have a week off with a bye.
Full time: Canberra Raiders 21 - 20 Manly Sea Eagles
Melbourne Storm deny North Queensland Cowboys fourth win of season
Cameron Munster's accuracy with the foot has rejected the North Queensland Cowboys of a rare victory in 2018, nailing a field-goal to win 7-6 in Townsville last night.
Johnathan Thurston missed an opportunity to level the scores with a field-goal of his own, but his attempt flew wide of the uprights in the closing stages of the game.
Melbourne Storm skipper Cameron Smith busted a Thurston tackle to score the first points of the game seven minutes before halftime.
Converting his own try, Smith's efforts enabled the Storm to take the lead into the break 6-0.
Cowboys flyer Kyle Feldt got the home side on the scoreboard 13 minutes into the second half following a skilful kick from Te Maire Martin.
Feldt lept over New South Wales Blues contender Josh Addo-Carr to touch down inside the sideline in the right-hand corner.
Thurston then slotted the conversion to level the scores.
Munster broke the deadlock with less than eight minutes left in the game before Michael Morgan missed a conversion attempt for the Cowboys.
Morgan thought he had later sealed the deal for his side when he crossed over the line, but the try was disallowed for an offside infringement from Jason Taumalolo.
The Storm's victory was marred by a cheap shot from Sam Kasiano on Thurston who had offloaded the ball to a teammate.
Kasiano snapped the North Queensland stalwart in half with a late tackle in the lower back - he was placed on report as a result.
The loss was the Cowboy's ninth for the season, having lost five of their past six games at 1300SMILES Stadium.
They will travel to Sydney to take on Manly next weekend while the Storm has a bye.
Full time: Melbourne Storm 7 - 6 North Queensland Cowboys
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