The Richard Childress driver grabbed the lead of the race during the seventh caution of the day, following an impressive stop after he had entered pit road in second place behind Michael Waltrip Racing's Martin Truex Jr.
Just as Harvick crossed the finish line first, grabbing five bonus points in the process, officials notified his team that the Californian had gone over the 49.9 mph absolute speed limit. Not only he was dropped to the tail end of the lead-lap cars, but also denied the bonus points for leading.
"I don't think that penalty will ever settle in my stomach," said Harvick. "When you read me off my pit road times of 49.6 [mph], 49.4, 50.8 and then 49.6; and there's only a handful people that get to see them, I won't ever settle for that.
"I don't know how you can be speeding when you're on the bumper in front of you if the other guy is not speeding. So that's about it."
While charging back through the field Harvick clashed with Joe Gibbs Racing's Kyle Busch, who had a couple of exchanges with him earlier in the day, hitting the RCR driver's rear bumper on an early restart and racing him aggressively for position a couple of times.
Twenty-three laps from the end, Harvick arrived on Busch's rear bumper, making contact with him at the exit of Turn 4 and sending the #18 Toyota spinning towards the inside wall.
"He raced me like a clown all day," said Harvick about Busch. "Three-wide, on the back bumper, running into me, and I just had enough."
The incident caused the final caution of the day, at which time title rival Denny Hamlin was a lap down following the final stops under green-flag conditions. That put the JGR driver all but out of contention for a top finish, boosting Jimmie Johnson's title hopes.
Harvick was still proud in the end about his overall performance this year, specially after a poor 2009 where RCR drivers failed to make it to the season play-off. He hopes his team can now consistently challenge for titles in the next few years, building on the foundations laid down this season.
"I remember where we sat when I left this race last year," said Harvick. "You always want to win but I'm not going to sit here and be disappointed. We raced as hard as we could race this year, with everybody putting up every piece of effort that they had, week in and week out, and I know what it feels like to run like we did last year.
"So I'm more excited about looking to be consistent and racing this way. I'm not going to look back. This is going to make us stronger. We have got a good race team that's going to stick around for a while, and I'm just happy to be a part of it right now."
Harvick's third place in the drivers' standings is his best finish in the championship following 10 full seasons in the Sprint Cup.
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