NASCAR issued the penalties against the Penske Racing teams after their Fords were found to have unapproved suspension systems before the April 13 race at Texas Motor Speedway.
Penske appealed to the three-member National Stock Car Racing Appeals Panel, but the panel unanimously upheld the penalties following a hearing attended by NASCAR officials and Penske executives.
Penske said it has one more appeal left that it will pursue next week, with John Middlebrook, NASCAR chief appellate officer.
The penalties included Keselowski and Logano each being stripped of 25 championship points.
Keselowski crew chief Paul Wolfe, Logano crew chief Todd Gordon and other team members were suspended for several races, although they can keep working until the appeals are exhausted. Wolfe and Gordon also were fined $100,000 apiece.
The next Cup race is Sunday at Talladega (Ala.) Superspeedway.