Menard grabbed the lead from defending champ Jamie McMurray with four laps remaining and then hung on to claim his first career Sprint Cup Series win in his 167th start.
Gordon, who has won Brickyard 400 four times, ended up in second place, with Regan Smith, McMurray and Matt Kenseth rounding out the Top 5.
Menard joined Trevor Bayne (Daytona 500), Smith (Darlington) and David Ragan (Daytona July race) as first-time Sprint Cup winners this year.
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