Crew chief Chad Knaus was fined $100,000 and suspended six races Wednesday, car chief Ron Malec also was barred for six races, and Johnson was docked 25 points, sending him into this weekend's race last in the Sprint Cup Series standings.
The penalties stem from a failed inspection Feb. 17 at Daytona International Speedway. NASCAR said the No. 48 Chevrolet had illegally modified sheet metal between the roof and the side windows, an area known as the C-posts.
Hendrick Motorsports immediately said it would appeal, and Knaus and Malec can attend races during the process.
"Our organization respects NASCAR and the way the sanctioning body governs our sport," team owner Rick Hendrick said. "In this case, though, the system broke down, and we will voice our concerns through the appeal process."
Should the penalties stand, Johnson finds himself in a huge hole at the start of the season. He was wrecked just two laps into Monday night's Daytona 500, and his 42nd-place finish put him 42nd in the standings with two points.
The penalty drops him to 43rd in the field, with minus 23 points. He's now trailing Daytona 500 winner Matt Kenseth by 70 points, and is 58 points outside the top 10.
It comes after Johnson's worst season in NASCAR: his streak of five consecutive championships was snapped last year, and he finished a career-worst sixth in the standings. He also won only one race.
Knaus, meanwhile, has run afoul of NASCAR before.
He's been suspended four previous times, but had a two-race ban in 2005 overturned in the appeals process. His last suspension was for six weeks in 2007 when NASCAR said he had flared out the front bumpers of Johnson's car at Sonoma.
His first suspension was in 2001, as crew chief for Stacy Compton, because NASCAR said he had unapproved shoulder harnesses in the car. Knaus teamed with Johnson at Hendrick Motorsports at the end of that season, and the two have gone on to 54 victories and five championships.
Johnson has a 55th victory, the 2006 Daytona 500, which was won while Knaus was serving a suspension. Darian Grubb filled in for that race.