The Richard Childress Racing team had appealed the stiff penalties handed down to Bowyer and both his crew chief and car chief after the opening race of NASCAR's Chase for the Championship.
Bowyer had jumped from 12th place to second in the points chase with the win, but his hopes for a Sprint Cup title were all but wiped out when his team was assessed a 150-point penalty.
Crew chief Shane Wilson and car chief Chad Haney were suspended for six races and placed on probation for the rest of the season. Wilson was fined $150,000. The sanctions came after Bowyer's car failed a post-race chassis inspection.
A three-member panel heard the appeal during a 5-hour hearing held Tuesday at NASCAR's research and development center.
Team owner Richard Childress said he would make another appeal to the governing body's Chief Appellate Officer John Middlebrook.
"I gave them the ($150,000) check and our appeal notice," Childress said. "We're going to appeal it to the commissioner (Middlebrook). We're very disappointed. We had proof."
Childress said last weekend the chassis was 0.06 of an inch out of alignment because a tow truck hit the rear bumper when the car was pushed into the winner's circle. Childress also said the rear bumper was hit by other drivers congratulating Bowyer for his victory.
The tow truck was used to push the car because it ran out of fuel before it could be driven back to the finish line.