Gordon, the four-time series champion, and Johnson, the defending Nextel Cup champion, were each docked 100 points. Crew chiefs Chad Knaus and Steve Letarte were both fined $100,000 and suspended for six races because their cars failed an initial inspection at Infineon Raceway.
The penalties are a blow to Hendrick Motorsports, which has 10 wins this season _ four each from Gordon and Johnson. Team owner Rick Hendrick said he was disappointed and called the punishment "excessive."
"Right now, all of our options are being evaluated, including our personnel situation and a possible appeal to the National Stock Car Racing Commission," Hendrick said in a statement. "We'll take some time to decide on a direction and make an announcement regarding our plans for New Hampshire later in the week."
The two Hendrick cars failed inspection Friday when NASCAR found unapproved modifications to the fenders on the COT. NASCAR refused to let either driver on the track the entire day, and neither was allowed to qualify.
The fenders were fixed, the cars passed inspection Saturday and were allowed to race Sunday. Gordon, the Nextel Cup points leader, finished seventh. Johnson was 17th.
Hendrick traveled to California after the failed inspection, and argued his crew chiefs were operating in a "gray area" of the rule book as it pertains to the NASCAR-mandated COT.
"I don't necessarily say they bent the rules," Hendrick said. "I think they thought they were working inside an area in which they could."
But NASCAR insisted its rules are black and white, with no wiggle room, especially on the COT.
"In the old days there was a gray area, in the new days ... it's not a gray area," said Robin Pemberton, vice president of competition. "We mean business with this car. There are similar things that could have been done to old cars and because the rules were so loose, we couldn't take a stand.
"But we owe it to the teams and the industry to uphold the standards of the Car of Tomorrow for the integrity of this sport."
NASCAR spent seven years designing the COT, and bills it as a bigger, boxier car that will improve safety, reduce team costs and improve competition. It was supposed to be phased into competition over the next three seasons, but now will be used exclusively next season.
The car made its debut in March, and NASCAR issued an official warning that any team caught tinkering with the car would be subjected to a loss of 100 points, a $100,000 fine and a six-race suspension.
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NASCAR adhered to those guidelines last month when it penalized Dale Earnhardt Jr. and his crew chief, Tony Eury Jr., for modifications found on the wing of their COT at Darlington Raceway.
Pemberton said the penalties to the two Hendrick cars was actually more severe than Earnhardt's because Gordon and Johnson were not given any track time on Friday at Sonoma.
"We're going to continue to ratchet up the penalties and this one is increased over the last penalty because these cars were parked on Friday at Infineon," Pemberton said. "It has been and will be a more severe hit to the teams if they continue to play loose with this Car of Tomorrow."
The penalties do little to either driver in the standings. Gordon is still the series leader, although his margin was cut to 171 points over Denny Hamlin, and Johnson dropped from third to fifth.
But under the Chase for the championship format, the top 12 drivers in the standings will race for the Nextel Cup over the final 10 events of the season. And, in a seeding twist introduced this year, drivers will start the Chase with 10 bonus points for every "regular season" victory.
Gordon and Johnson have each won a series-best four times this season, and barring a total collapse, both will qualify for the Chase and start it with a comfortable lead.
But the team will have to prepare for its title chase without their crew chiefs, who are not eligible to return to the track until the Aug. 19 event in Michigan. If they inform NASCAR of their intent to appeal, Knaus and Letarte can work this weekend at New Hampshire, site of the Sept. 16 Chase opener.
This is the first major violation for Letarte, who started sweeping floors at Hendrick and rose through the ranks to become Gordon's crew chief with 10 races to go in 2004.
But Knaus is a repeat offender, and this is his fourth suspension since 2001. He sat out four races last season when NASCAR found illegal modifications following Johnson's qualifying run for the Daytona 500.
Johnson went on to win the 500, and again at Las Vegas, without Knaus. The two reunited in March and went on to win their first championship.
Pemberton said there was no thought given to handing Knaus a stiffer punishment based on his past record.
"Chad has served his time and he's been good since Daytona of '06," Pemberton said. "This is about a new era going forward with the Car of Tomorrow. We've basically started over, and people have been warned."