Ireland’s Sam Bennett (Deceuninck-Quick-Step), who won Tuesday’s 10th stage and was hoping for a victory in Poitiers where compatriot and friend Sean Kelly won on the Tour in 1978, took second place.
Sagan, who was excluded from the 2017 Tour de France after elbowing Briton Mark Cavendish in a sprint finish, was also docked 13 points for his dangerous move.
“We accept the jury decision. We always aim to win, but in a respectable way, even when the adrenaline is high in a Tour sprint finish,” Bora-Hansgrohe team said in a statement.
Bennett extended his lead in the points classification to 68 points, boosting his hopes of securing a first green jersey for Ireland since Kelly in 1989.
Slovenian Primoz Roglic (Jumbo-Visma) retained the overall leader’s yellow jersey after a quiet day in the main bunch.
He leads the defending champion, Colombian Egan Bernal (Ineos Grenadiers), and Frenchman Guillaume Martin (Cofidis) at the end of a dull stage in which Martin’s compatriot Matthieu Ladagnous (Groupama-FDJ) was the lone breakaway rider.
Thursday’s 12th stage is a 218-kilometre parcours from Chauvigny to Sarran.