British rider Adam Yates was moved to first place in the revised general standings after Alaphilippe was docked 20 seconds. TV footage showed the French rider grabbing a bottle from a staff member of his squad about 18 kilometers (11 miles) from the finish.
Riders are not allowed to receive provisions during the final 20 kilometers (12.5 miles) of a stage.
Yates now tops the standings with a three-second lead over Primoz Roglic. Alaphilippe dropped to 16th overall, 16 seconds behind the new leader.
Belgian rider Wout van Aert won the fifth stage in a sprint finish.