The Movistar rider finished second at the Giro d'Italia to Tom Dumoulin despite leading going into the final day's time trial.
The Colombian had hoped to become the first person since Marco Pantani in 1998 to win the Giro-Tour double.
His exertions at the Giro, though, have meant that he has opted against racing the Route du Sud (June 15-18).
In light of his efforts in the opening Grand Tour of the season, and the fact that there are only 34 days between the end of the Giro in Milan and the beginning of the Tour in Düsseldorf in July 1, Quintana believes that he is better placed to recover at home and prepare for the Tour through training as opposed to racing.
The exclusion of any races before he takes on defending champion Chris Froome (Sky), Richie Porte (BMC Racing) and Alberto Contador (Trek-Segafredo) in La Grand Boucle isn't entirely surprising, although there remained a chance that he would race at least once.
Quintana won the Route du Sud last year and many expected him to give Froome a closer challenge in the Tour, but he was unable to counter the Brit's intuitive tactics and time trialling, eventually settling for third place behind Romain Bardet (AG2R La Mondiale) in second.
Quintana, 27, has won both the Giro and Vuelta a España but a maiden Tour win remains his number one priority.
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