Tranmere moved above Stockport in the top-half of the League One table after defeating the Hatters at Prenton Park.
Stockport keeper Owain fon Williams made first-half saves from Chris Shuker and Edrissa Sonko but could not stop Gareth Edds heading home a corner.
Fon Williams made further saves from Sonko and Ian Moore - but Moore eventually scored from the spot after he was fouled by Greg Tansey.
Oli Johnson scrambled an injury-time consolation from Tommy Rowe's corner.
Tranmere: Coyne, Shotton, Chorley, Goodison, Taylor, Edds, Sonko, Jennings, Barnett (Savage 81), Shuker, Moore. Subs Not Used: Achterberg, Cresswell, Ahmed, Henry.
Booked: Goodison.
Goals: Edds 57, Moore 90 pen.
Stockport: fon Williams, Mullins, Raynes, Tunnicliffe, McNulty, Baker (Tansey 81), Blizzard, Mainwaring (Johnson 64), Rowe, McSweeney, Turnbull. Subs Not Used: Threlfall, Vincent, Pilkington.
Booked: Baker.
Goals: Johnson 90.
Att: 5,259
Ref: Neil Swarbrick (Lancashire).
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