Gordon radioed his crew chief with less than 50 laps remaining saying he was experiencing a bad vibration, and when he made his final pit with 41 laps to go his team made adjustments to the car.
He grabbed the lead for good after a cycle of stops under green ended with 38 laps left and then held off a furious challenge from his Hendrick Motorsports teammate, Jimmie Johnson, during the closing laps.
Gordon finished 0.6 seconds ahead of Johnson for his third win of the season and 85th in the Sprint Cup Series, giving him sole possession of third on the series' all-time race winners list.
Tony Stewart finished third, keeping him in the 10th spot on the Chase for the Sprint Cup points list with only one race to go.
Kurt Busch was fourth, followed by Carl Edwards and Brad Keselowski.
The race was originally set for Sunday was pushed back to Tuesday due to Tropical Storm Lee.