Pinot lined up at the Vuelta in the hopes of taking a consolation prize from 2020, but after losing 25 minutes in the opening two stages he has pulled out of the race.
Groupama-FDJ said before stage three: "Despite the rest period he observed, the first two stages of the Vuelta have shown Thibaut Pinot continues to suffer from the back pain he experienced after his crash at the Tour de France.
"With regard to the next season, priority is given to his complete recovery - he will not take the start of the third stage and will no longer compete in 2020."
In his pre-race race press conference, as reported by Cycling News, Pinot said he had not recovered from his crash on stage one in Nice, and said he would be supported his team-mate David Gaudu in the general classification race.
The 30-year-old said: "Since the Tour, my back has not recovered 100 per cent.
"I don't want to end the year at the Tour, and I hope the Vuelta can put me back on the right path, and help me into the winter. I'm counting on the Vuelta to give me the enjoyment that I've not had for quite a while now."
Pinot's misfortune in Grand Tours continues, after a string of huge disappointments in three week races, which started at last year's Tour de France.
The Frenchman has been among the strongest contenders in last year's Tour, but suffered a muscle tear in the final week and abandoned the race in tears on stage 19.
In the 2020 Tour, Pinot looked to be in great form after finishing second in the Critérium du Dauphiné, but his dreams of the yellow jersey fell to pieces on the opening stage of the Tour.
Pinot was caught in a crash in the closing kilometres of stage one in Nice and suffered a back injury when another rider hit him.
He made it through Paris despite the injury, finishing 29th overall, before lining up in Spain a month later.
But as the injury still lingered, Pinot lost 10 minutes on the brutal opening stage of the Vuelta in the Basque Country,
He then lost another 15 minutes on stage 10, before deciding not to take to the start of stage three.
Groupama-FDJ's general classification hopes for Gaudu have also taken a blow, as he sits 3-20 down on the leader after two stags.