The race leader was looking at the prospect of another day in yellow after an armchair ride on a sleepy stage for the peloton on the 183-kilometre stage from Gap to Privas.
Alaphilippe finished within the peloton and it appeared that it was another day in yellow ticked off for the Frenchman.
However, French television cameras had caught Alaphilippe taking a bidon from a soigneur on the side of the road with just over 17 kilometres remaining to the finish.
Rule 4.10.4 of the UCI regulations regarding road races forbids feeding within the final 20 kilometres of the stage, with a 20-second penalty and a 200 Swiss franc fine the nominated penalty.
“I’m waiting for confirmation," said Alaphilippe while waiting near the podium. "Apparently, I took a feed in a non-authorised zone. That’s a 20-second penalty so it’s Yates in the yellow jersey, normally. If that’s the case, that’s how it goes. It’s the decision of the jury so I can’t do anything about it.”
“I had to stay concentrated to defend the jersey and try and win the stage with Sam [Bennett], who’s in green, which is good news,” Alaphilippe added. “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.”
The time penalty sees Alaphilippe now 16 seconds down on the new race leader, Adam Yates (Mitchelton-Scott), who looked a bit bemused taking to the podium in yellow.
Yates did some interviews after the stage, echoing the sentiments of many as he took yellow in less than optimal circumstances.
"I don’t think any rider would want to take yellow under these circumstances," said Yates. "I’d prefer to take it with my legs rather than the result of a time penalty. I didn’t even find out until I was in the bus and showered. I feel bad for him.”
Alaphilippe now sits 16th overall, 16 seconds behind Yates with a summit finish on Mont Aigoual set for riders on the next stage.
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.