Defending Sprint Cup champion Keselowski had four team members suspended for six points races, while Logano lost three members of his crew. The drivers were docked 25 points each, as were the car owners.
The points penalty dropped Keselowski from second to fourth in the Sprint Cup standings, while Logano fell from ninth to 14th.
Penske Racing vowed to appeal.
"Penske Racing will appeal utilizing the appropriate NASCAR process," the team said. "We have no further comment at this time."
NASCAR said both Penske cars used parts that had not been approved and NASCAR inspectors confiscated the original rear-end housing from Keselowski's No. 2 Ford and Logano's No. 22 before Saturday night's race. Logano was late to the starting grid because of the additional inspections and he had to start at the back of the field. He finished fifth and Keselowski was ninth.
NASCAR suspended Keselowski crew chief Paul Wolfe and three others for six points races, plus the non-points All-Star race, and fined Wolfe $100,000. Logano crew chief Todd Gordon received the same fine and he and two other crew members received the same suspensions.
NASCAR also penalized Martin Truex Jr., who finished second at Texas behind Kyle Busch, for having a front end that was too low. He and owner Michael Waltrip were each docked six points and crew chief Chad Johnston was fined $25,000.
Keselowski was livid following the race.
"The things I've seen over the last seven days have me questioning everything that I believe in, and I'm not happy about it," Keselowski said. "I have one good thing to say, and that was my team and the effort they put in today, in fighting back with the absolute (expletive) that's been the last seven days in this garage area."
Keselowski, who has six top-10 finishes, got a penalty a week earlier at Martinsville for pitting outside his stall. He still disputes that.
"There's so much stuff going on. You guys have no idea ... what's going on," Keselowski said. "I could tell you there is nobody, no team in this garage with the integrity of the 2 team. And the way we've been treated over the last seven days is absolutely shameful."
Keselowski then spent Tuesday at the White House, where President Barack Obama honored him and his crew for winning the Sprint Cup championship.