The right front fenders above the wheel well on both the No. 24 Chevrolet of Gordon and the No. 48 Monte Carlo of Johnson were too wide for Car of Tomorrow specifications.
Both drivers will have to start at the rear of the field for Sunday's Toyota/Save Mart 300 on the 2-mile Infineon road course.
Nextel Cup series director John Darby clearly was furious about the extent of the violations.
"It's unprecedented," Darby said.
Both teams made repairs to their primary cars and resubmitted them for inspection Friday afternoon. But neither car will be given the OK to compete until Saturday morning.
"Nothing is going to ruin my week," said Gordon, who became a father Wednesday when his wife (Ingrid Vandebosch) delivered their daughter, Ella Sofia. "I'm on cloud nine.
"But this definitely put us in a box we're going to have to work out of. This is a big deal and it's going to be tough."
Gordon, the season points leader, won at Infineon one year ago. His five victories at Sonoma are the most among active drivers.
But starting from the back is a big problem on a road course, where passing is difficult. No driver ever has won this race from the rear of the field. The worst starting position for any winner at Infineon was 13th by Davey Allison in 1991.
"Obviously, this is a big setback," Johnson said. "But what happened today we can't get back. What we have to do now is make sure we leave here today with our team as a unit and tough this out."
Hendrick Motorsports has 10 victories in 15 Nextel Cup races this season. The organization also has won five of the six COT races this season. Gordon and Johnson each have two victories in the COT.
Winning cars are inspected by NASCAR officials immediately after each victory.
"Because of that, we've probably been under more scrutiny of our COT cars than any other team," said Doug Duchardt, vice president of development for Hendrick Motorsports. "We did not receive any warning about this."
But Duchardt admits the cars were deliberately altered before for this event.
"The cars fit the template,' he said. "The problem was the area between the templates. We felt we could work in between the templates. We found out today that is not the case."
The right front fender on both cars were flared out above the wheel. Both teams repaired the cars by taking a mallet and banging those fenders back in, causing a small hump on the hood above the wheel.
"This car [the COT] is an evolution," Duchardt said. "When NASCAR sent the templates for the COT, they also sent data to define the car in its entity. They say we don't fit that data. That's why we are in this situation."
Neither crew chief -- Steve Letarte for Gordon and Chad Knaus for Johnson -- was suspended Friday. But additional penalties for the drivers and crew chiefs are likely next week.
NASCAR officials have warned all the teams that any violations involving the COT would result in severe punishment.
The No. 8 Chevy team of driver Dale Earnhardt Jr. was the first team to receive a major penalty for a COT violation. An initial inspection at Darlington, S.C. in May showed the brackets on the rear wing were modified outside regulations.
Earnhardt was penalized 100 points. Crew chief Tony Eury Jr. was suspended for six races and fined $100,000.
Letarte wouldn't say if he expected to be suspended.
"Anything at this point is an assumption," Letarte said. "I'm sure on Tuesday we'll find out about that."
Knaus was suspended for the first four races last season for a body violation at Daytona. Johnson went on to win his first Nextel Cup championship.
Knaus was surprised about NASCAR's decision Friday.
"There's a span of about 10 inches [between templates] that we thought were not governed," Knaus said. "We thought we had found a little more downforce. But it seems we went into an area where NASCAR doesn't want us to go."
NASCAR spokesman Ramsey Poston said that should have been obvious.
"The whole point of the COT is to eliminate these types of modifications," he said.
Terry Blount covers motorsports for ESPN.com. He can be reached at email@example.com.