The 2019 Tour de France champion was seventh on GC after three stages, 31 seconds behind race leader and expected Tour de France rival Primoz Roglic (Jumbo-Visma).
Bernal had consistently lost seconds to Roglic on the summit finishes on stages 2 and 3 but was the strongest at Team Ineos, with both Chris Froome and Geraint Thomas distanced on the final climbs.
Leaving the race with two stages remaining raises questions over whether the Colombian will be able to complete Tour de France recon rides with his team over the coming weeks and his eventual form for the most important Grand Tour of the 2020 season.
"He doesn't start today," teammate Geraint Thomas confirmed at the start of stage 4.
"He's got a bit of a bad back and the best thing for him is to just take it easy. It's such a short turn around to the Tour that it's important he gets it 100 per cent right and be good then. I don't think it's a major issue, it's just better to be on the side of caution. He's had two races before this as well, so he's got the racing that he needs. It's just about making sure that everything is 100 per cent there and that there are no issues."
Roglic appeared surprised by the news surrounding Bernal but admitted that the race was still far from over, with many top climbers within touching distance of the yellow jersey.
"I don't think that this changes much for us. We need to focus on our work and try to be the best. I'm looking forward to this stage. We'll still see a hard race, it's not everything on Egan because we have a lot of really strong guys. It's going to be hard racing. I'm not sure what will happen today but it will definitely be hard racing. There are mountains from the beginning but for us, we want to have control and a good situation. We'll try and focus on that," Roglic said.
The loss of Bernal leaves Team Ineos without a GC leader for the race. Both Thomas and Chris Froome have lost significant time, while the team's best-placed rider in the overall standings is Pavel Sivakov, who sits in 18th place at 3:15.
Follow live coverage from stage 4 of the Criterium du Dauphine.
More to follow…
Stage four of the #Dauphine is set to begin shortly. We can confirm @Eganbernal will not take the start this morning in Ugine. pic.twitter.com/uRLT6NHu2pAugust 15, 2020
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