Alaphilippe had led Yates by four seconds when the race was finished and looked to have retained the yellow jersey, but television footage showed him taking a bottle from a Deceuninck-Quick Step team support member with 17.8km to go - under the rules of cycling's world governing body UCI, riders are not allowed to take on food or drink in the final 20km of a race.
Flamengo netted twice in quick succession after the restart: first with a stunning first-time effort from playmaker Everton Ribeiro and then with a cool Arrascaeta finish after a counterattack.
It was a bizarre way for the Frenchman to lose the jersey which he had kept for three days after winning the stage two.
Earlier, sixth seed Petra Kvitova of the Czech Republic edged past Ukraine's Kateryna Kozlova 7-6 (3), 6-2, and eighth seed Petra Martic of Croatia beat fellow Ukrainian Kateryna Bondarenko 6-3, 6-4 to also advance into third round. Enditem
"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.
Klein is expecting the many young talents to continue their performance. He mentioned Dortmund's Erling Haaland as one of the examples next to Jadon Sancho.
Brazil are currently eighth in the FIFA women's world rankings, behind the US, Germany, France, Netherlands, Sweden, England and Australia. Enditem
Despite the Bavarians having dominated the national and international stage, close competition is secured as domestic competitors such as RB Leipzig, Borussia Monchengladbach, Bayer Leverkusen and Borussia Dortmund have caught up over recent years.
He said he was looking forward to battling for his place alongside players such as Paul Pogba, Bruno Fernandes, Nemanja Matic and Fred.
"I rode my tempo and gave it all to create a gap big enough to win."
Bayern remains the league's flagship from an international perspective, the official underlined.