The Belgian Van Petegem would have finished third at Paris-Roubaix had he not been disqualifed, along with compatriot Leif Hoste and Russian Vladimir Gusev (respectively second and fourth across the line), for passing a downed train crossing.
"Several mistakes have been clearly done by various parties during and after the race, with the result that Peter Van Petegem has lost a fine place on the podium," Davitamon said on their official website.
"Davitamon-Lotto has decided this afternoon to lodge an official written protest by the UCI against the result of yesterdays Paris-Roubaix."
Bennett takes 50th pro win on Stage 4 at UAE Tour
Van Petegem, who won the race in 2003, said both he and the race organisers were at fault.
"I know all too well that you have to stop when you are in front of a closed red-light railway crossing," the Van Petegem told Belgian newspaper De Morgen.
"I myself hit the brakes, but Hoste kept on going, Gusev followed and what does one do in a situation like that but follow? What if Cancellara had been in front of the closed railway passage and lost the race because of it?"
"I agree we made a mistake, but the organisers are not without fault either," he added.
Davitamon's website specifically mentioned the points the team would be cost as one reason why it decided protest after reviewing tapes of the race.
"Besides the individual Pro Tour points lost by Peter," Davitamon said, "these decisions also influence the teams classification, and the position of the coaches for the coming Pro Tour events.
World champion Tom Boonen, who finished in second at Paris-Roubaix thanks in part to the ruling, questioned the bizarre appearance of the train on Sunday, and Van Petegem echoed those sentiments to the Belgian paper.
"I think it's strange that we have to cross a railway so close to the finish," Van Petegem said. "At that moment we were still riding flat out chasing for the victory - Cancellara was not outside of our reach as yet."
"To take a decision like that after six hours of racing is hard. On top of that we didn't put anyone in danger; not ourselves, not others."
Tour of Turkey
GC favourites crash ahead of Queen Stage
Tour of Turkey
Caleb Ewan claims Tour of Turkey Stage 4