Julian Alaphilippe lost his Tour de France yellow jersey on stage four after being handed a time penalty.
There is no official confirmation about why Alaphilippe was punished, but Yates now moves into the race lead.
Reports suggest that Alaphilippe was handed a 20-second penalty for taking a bidon from a roadside helper inside the final 20km of the stage.
According to the Tour organisers, the commissaires made the decision to punish Alaphilippe after he made an "unauthorised supply pick-up."
Video footage has since emerged of Alaphilippe taking a bottle from team staff with around 17km of the stage left to race.
UCI rules state that all feeding outside the feed zones, either from a car or on foot, is strictly forbidden inside the first 30km of a stage and inside the last 20km.
Alaphilippe now slips down to 16th place overall, 16 seconds behind Yates.
Primož Roglič (Jumbo-Visma) now sits second, three seconds behind Yates while Tadej Pogačar (UAE Team Emirates) is third, seven seconds off the lead.
An official statement from the organisers said: "Following the commissaries' decision, Julian Alaphilippe receives a sanction of 20 seconds for an un-authorised supply pick-up. Adam Yates is the new wearer of the yellow jersey."
UCI regulation 2.3.027 says: "All feeding (from a car and on foot outside of the feeding zones signposted by the organiser) is strictly forbidden: during the 30 first and last 20 kilometres; in the last 500 meters before a sprint counting for a secondary classification (points classification, king of mountain classification or others), bonus sprint, feeding zone; in the first 50 meters after a sprint counting for a secondary classification (points classification, king of mountain classification or others), bonus sprint, feeding zone; on descents of mountains listed on the mountain classification; in any other area specified by the organiser or the commissaires panel.
"The commissaires panel may adapt the distances mentioned above, depending on atmospheric conditions and the category, type and length of the race. Such a decision must be communicated to the followers through radio-tour."
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