NASCAR said that in its post-race inspection of Kenseth's No. 20 Toyota, it found the car had an unapproved engine part -- a connecting rod that was too light.
Although Kenseth was able to keep his victory, the driver was stripped of 50 Sprint Cup Series championship points, dropping the former Cup champion from eighth in the standings to a tie for 14th with Jeff Gordon.
It's the first time a Cup driver has been docked 50 points since NASCAR adopted a new championship points format in 2011, NASCAR said, adding that the penalty was equivalent to roughly 200 points under the old format.
NASCAR also took away the three bonus points Kenseth's win would provide the driver if he is among the top 10 drivers qualifying for NASCAR's Chase for the Cup late-season title playoff.
In addition, Kenseth's crew chief, Jason Ratcliff, was fined $200,000 and suspended for the next six point-paying Cup races, a period that includes the non-points Sprint All-Star Race on May 18.
Gibbs Racing said it planned to appeal the penalties.
The engine was built by Toyota Racing Development (TRD) in Costa Mesa, which said the rod "weighed in approximately three grams under the legal limit."
"We take full responsibility for this issue," TRD President Lee White said in a statement. "It was a simple oversight on TRD's part and there was no intent to deceive or to gain any type of competitive advantage."
Kenseth, who joined Gibbs Racing this season, won from the pole at Kansas Speedway and led 163 of the race's 267 laps.
It's the second time in as many weeks that one of NASCAR's leading teams has been hit with stiff penalties.
Reigning Cup champion Brad Keselowski, his Penske Racing teammate Joey Logano and several of their crew members were penalized because their Fords had unapproved suspension systems before the race at Texas Motor Speedway.