The FDJ.fr rider had "the worst day of his life as a cyclist" on stage 4 and suffered through the hot first week of the race but the stage to San Miguel de Aralar proved to be the final straw.
"At the beginning of the stage, I tried to catch the breakaway, but I realised that I was about to stop," he told L'Equipe. "After 50 miles, there was a crosswind, I had no more strength. It was the same feelings at the beginning of this Vuelta."
Last year Pinot was seventh overall although he entered the race this year with no expectations of a high GC result after his third place at the Tour de France in July.
The 24-year-old was focused on recording a stage win with his sole 'victory' this year being the best young rider classification jersey at the Tour. Pinot's only win remains his 2012 Tour stage victory.
Almost an hour down on race leader Alberto Contador (Tinkoff-Saxo) when he abandoned, Pinot had persevered despite suffering from a fever and explained that his thoughts on making a recovery proved to be false.
"I thought maybe after the rest day and the time trial, I would be better," he said. "But I had not recovered from the virus that caused me fever for three days, [the race is] not worth pursuing."
Pinot added that he hopes to be back racing next weekend but will first enjoy a small period of rest and recovery.
"I'm going home to rest two or three days, and hope to be fit for the Tour du Doubs [September 14] in ten days."