Phil Jagielka headed Everton's first win of the season at Deepdale.
After losing to FC Sion and Cambridge, Jose Baxter signalled Everton's intent by hitting the bar with a free-kick.
And David Moyes' side grabbed the winner against his old club when Jagielka nodded home a corner from 16-year-old Baxter after eight minutes.
Mikel Arteta came on for the final half-hour as he continues his comeback from a groin injury.
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Wigan lost 2-0 to Bundesliga side Eintracht Frankfurt in Austria. Steve Bruce's new signings Daniel de Ridder and Olivier Kapo featured.
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