The Colombian was seventh overall after losing a bit of ground to leader Primoz Roglic of Slovenia and second-placed Thibaut Pinot of France in the two previous stages.
"We can confirm Egan Bernal will not... start this morning in Ugine," Bernal's Team Ineos said on Twitter.
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Considered the main warm-up race for the Tour, which starts on August 29 in Nice, Ineos have seen disappointing results so far on the Dauphine, with both Bernal and four-time Tour winner Chris Froome far from their best.
Ineos gave no reason for Bernal's absence, though French sports daily L'Equipe reported that the 23-year-old was suffering from back pains decided to take time out to rest ahead of the Tour.
"I don't think it's a major problem, but it's best to be cautious," his team mate and 2018 Tour winner Geraint Thomas was quoted as saying by the newspaper.
Bernal's withdrawal follows success in La Route D'Occitanie at the beginning of the month.

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Additional reporting by Reuters.
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