The Richard Childress driver has been docked 150 points in the standings, after his #33 Chevrolet failed to pass a detailed inspection at NASCAR's Research and Development facility in Concord, North Carolina, where the car was taken following the initial post-race inspection at the track.
Officials found discrepancies in the "car body location specifications in reference to the certified chassis", citing that these "did not meet NASCAR-approved specifications." The NASCAR rulebook states how the bodywork must be placed in reference to the chassis and in the rear of Bowyer's car measurements were found not to comply.
Last week after the final race of the regular season at Richmond, Bowyer's team had already been warned about issues that arose during inspection of the car he ran at the event where he secured his place in the championship play-off. Officials found the Richmond car, which was selected randomly for inspection at the track, was too close to the mandated tolerances.
"Details regarding the #33 car surround the car from a post-race inspection after the Richmond race," said NASCAR's vice president of competition Robin Pemberton.
"We reinforced the fact that they had come exceedingly close to the measurements that we allow for post-race [inspection]. The #33 car that was raced in New Hampshire was brought back to the R&D centre after the race and that car did not meet specifications, as a result these penalties have been issued."
The points penalty has dropped Bowyer from second place in the Chase down to 12th and last among the title contenders, placing him exactly where he was before taking his first win of the season last Sunday, although with a larger gap to leader Denny Hamlin.
While Richard Childress was also docked 150 points in the owners' standings, crew chief Shane Wilson and car chief Chad Haney have been suspended for the next six races, Wilson additionally being fined $150.000.
There was no word from NASCAR regarding the cars run at Loudon by Bowyer's team-mates Kevin Harvick and Jeff Burton, which both passed inspection following Sunday's Chase opener.
Scott Miller, current director of competition at RCR and former crew chief for Bowyer's team-mate Burton, is expected to replace Wilson in his role while he serves his suspension.
The team has announced that it will appeal against the penalties.