"Team Sunweb have decided to withdraw Warren Barguil from the Vuelta a España," the team said in a statement.
"The 25-year-old talented rider, a winner of two stages and the mountains jersey at the Tour de France, openly expressed that he didn't wish to conform to team goals, which left Team Sunweb with no other option than to take this decision,"
The Frenchman was 13th overall after seven stages, one spot above designated team leader Wilco Kelderman of the Netherlands, who lost 17 seconds on Friday after the Dutchman suffered a puncture and Barguil failed to help him.
Barguil is leaving Sunweb at the end of the season to join French outfit Fortuneo-Oscaro.
"I have to leave the Vuelta by the decision of the team. I feel very well and have good legs," Barguil said in a statement.
"I see myself in a different role and am eager to attack in the mountains, as I did in the Tour. The Vuelta is a great race and it is disappointing to leave but this is a decision from the team that I need to accept."
Sunweb added that Barguil would continue with his race programme after the Vuelta.