Under racing rules, riders are not allowed to receive provisions — either drinks or food — during the final 20 kilometres (12.5 miles) of a stage. Deceuninck-Quick Step did not immediately explain why the staff member was posted inside that zone and why he handed out the bottle to the French rider.
Cycling's governing body, the UCI, said in a statement that two other riders, Sepp Kuss and Carlos Verona, were also penalized 20 seconds for the same offense.
"The absence of feeding in the last 20 kilometres is a rule that the teams are familiar with and that prevents that the feeding doesn't disturb the race at the entrance of the last kilometres," the UCI said.
Alaphilippe's teammate Dries Devenyns said the jury's decision was harsh.
"There is no time gain in taking a bottle from the side of the road," he wrote on Twitter.
Yates now tops the standings with a three-second lead over Primoz Roglic. Tadej Pogacar, another Slovenian rider, stands third, four seconds further back. Alaphilippe dropped to 16th overall, 16 seconds behind the new leader.
Alaphilippe waived to the crowd as he left the finish area without the race leader's jersey he had worn for the last three stages.
"It was a very long and very boring stage, with a very nervous finale. I had to stay concentrated to defend the jersey," said the Frenchman, who is not seen as a contender for the overall victory. "But if that's how it is, then no worries, tomorrow I'll pick myself up and we won't talk about it anymore."
The jury's decision overshadowed Van Aert's second career stage win at cycling's marquee event, a day after he produced a tremendous effort in the Alps in support of Roglic, his Jumbo Visma team leader.
Van Aert used his power in the slight uphill finish to win by half a wheel ahead of Cees Bol and Sam Bennett.
"It was a heavy finish. It was maybe the most easy stage I ever did in a cycling race because there was no breakaway, not a high pace at all, but then the last hour was really hectic with the wind," Van Aert said.
The Belgian abandoned the Tour last year with a serious leg injury that kept him sidelined for several months. But the three-time cyclocross world champion has been in superb form since the cycling season resumed last month, posting victories at the Strade Bianche, Milan-San Remo, as well as a stage win at the Criterium du Dauphine.
A humble rider regarded as a future great, Van Aert will now return to his "domestique" role, as a support rider for Roglic and other teammates.
"With a lot of happiness," he said.
Sandwiched between the race's first summit finish in the Alps and Thursday's tough climb up Mont Aigoual, the 183-kilometre stage through the Drome Provencale region gave the peloton a chance to relax a bit.
The stage started from Gap at a moderate pace under a bright sunshine, with riders talking to each other inside the peloton as they gently rode toward Privas, the French town famous for its chestnut cream.
French hope Thibaut Pinot, who crashed heavily during the opening stage last week, made the most of the pedestrian tempo to have his shoulder checked by the race doctor, then returned inside the pack without problem.
The strong headwinds deterred attacks and the race only heated up with 35 kilometres left when the big teams moved forward and jostled for position at the front to make sure they did not get caught in crosswinds. Kuss, an American riding in support of Roglic, crashed in the peloton but was able to resume racing and did not lose time.
The Tour, which was postponed from its usual July slot due to the coronavirus, ends in Paris on Sept. 20
