Alaphilippe took a 20-second penalty for accepting a bottle within the final 20 kilometres, seeing him drop to 16th on the general classification, 16 seconds behind new race leader Adam Yates (Mitchelton-Scott).
The French star took the news well and didn't appear ill-tempered or frustrated after the race, commenting before the penalty had been confirmed, '"But, voilà, if that’s how it is then no worries, tomorrow [Thursday] I’ll pick myself back up and we won’t talk about it anymore.”
For the rest of the race and the viewing public there was confusion as Yates was rushed to the podium and Alaphilippe rode off to his team bus.
"It's a pity to lose yellow like this," said Tom Steels. "We know about the 20-kilometre rule, it was quite dangerous at 70kph, then there was a flat part to get in position for the climb. It was the only spot we could still give a bottle.
"It's a special Tour, everybody has to be careful with the bottles and we have to stay away from the public also. So there were some circumstances that we missed the 20-kilometre mark by two kilometres. We made a mistake. There's nothing to do about it."
Deceuninck-QuickStep is operated by the bombastic Patrick Lefevre who accepted the penalty, but was not happy with his team staff.
"It's very hard but there is a rule," said Lefevre in an interview with Le Parisien, "and if we apply it severely to others, then it's the same for us."
"The yellow jersey is not above the others. If nobody warned the riders that we could refuel after the last twenty kilometres, then that's what is forbidden. Everybody knows that. But obviously someone at home didn't know that."
Deceuninck-QuickStep is renowned for being a tightly-run ship, with Lefevre most concerned that it was a Belgian staff member that had made the error.
"Of course, cycling means losing your jersey if you fall, have a flat tire, a mishap or if you come across someone stronger than yourself," he said. "But to lose it for such stupidity... What's more, the person who committed this stupidity is from back home [Belgium].
"Then nobody can be happy. I am not. Julian didn't deserve to lose it like that but the rules are the same for everyone. It's unbelievable. At the finish, we had two jerseys: yellow for Julian and green for Sam Bennett. And suddenly, we have only one again."
The Tour de France continues tonight with a 191-kilometre stage from Le Teil to Mont Aigoual, with the broadcast starting from 9.00pm (AEST) on the SBS ŠKODA Tour Tracker App, then from 9.30pm (AEST) on SBS and SBS On Demand.