Jordan Morton's goal secured Cowdenbeath's first away win of the season and dented Dundee's hopes.
The Dens Park side started the day top of the Scottish Championship but fell behind when Kane Hemmings atoned for a first-half penalty miss by firing home.
Jim McAlister slotted in from a Nicky Riley pass to draw the hosts level.
But Morton regained the lead for Cowden when he finished from six yards, giving Jimmy Nicholl his first win since returning to the club as manager.
And Dundee slip to second in the division with Hamilton moving top.
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