Four-time Tour de France winner Froome, who was involved in a high-speed crash at last year’s Criterium which almost cost the Team Ineos rider his career, finished in 49th place, 8 minutes 32 seconds behind Jumbo-Visma’s Roglic.
Slovenian Roglic attacked 650 metres from the finish line to leave France’s Thibaut Pinot in second spot and Germany’s Emanuel Buchmann in third.
Reigning Tour de France champion and Froome’s Ineos team-mate Egan Bernal sits fourth in the overall rankings after finishing 10 seconds back in 10th on Thursday.
By the time Roglic crossed the line rain had started to fall, and not long after a powerful hail storm described by Israel Start-Up Nation as “worse than anything we experienced” crashed down on the remaining riders.
“The scene was total chaos and mayhem… riders running for cover, hit hard by icy mini ping pong balls,” the team said on Twitter.
Some riders had to get off the bikes and walk to the finish as huge hail stones crashed down and quickly left the road covered in ice.
Jumbo-Visma’s Tony Martin was saved by a trackside fan who handed him an inflated rubber raft to protect himself from the falling ice balls.
This season’s Dauphine has been shortened and moved due to the coronavirus pandemic.
Friday’s 157-kilometre (97.5-mile) third stage heads east from Corenc near Grenoble to the Alpine village of Saint-Martin-de-Belleville.
The Tour starts on August 29 with Froome’s participation yet to be confirmed by Ineos before he leaves for Start-Up Nation at the end of the campaign.
“It’s incredible to be back in the peloton, but keeping in mind I’ve only had a handful of days racing in over a year’s time now,” he said.
“Obviously I’m still finding the race rhythm but I’m feeling better and better as I do more days of racing. I’m feeling optimistic about the Tour.”
Stage result:
1. Primoz Roglic (SLO/JUM) 3hr 39min 40sec, 2. Thibaut Pinot (FRA/FDJ) at 8sec, 3. Emanuel Buchmann (GER/BOR) same time, 4. Guillame Martin (FRA/COF) s.t., 5. Nairo Quintana (COL/ARK) at 10sec, 6. Miguel Angel Lopez (COL/AST) s.t., 7. Daniel Martinez (COL/EF1) s.t., 8. Mikel Landa (ESP/BAH) s.t., 9. Richie Porte (AUS/TRE) s.t., 10. Egan Bernal (COL/INE) s.t.
Selected others
13. Romain Bardet (FRA/ALM) at 59sec, 32. Geraint Thomas (GBR/INE) at 2min 53sec, 49. Chris Froome (GBR/INE) at 8min 32sec
General classification:
1. Primoz Roglic (SLO/JUM) 9hr 7min 12sec, 2. Thibaut Pinot (FRA/FDJ) at 12sec, 3. Emanuel Buchmann (GER/BOR) 14, 4. Egan Bernal (COL/INE) 16, 5. Guillame Martin (FRA/COF) 18, 6. Nairo Quintana (COL/ARK) 20, 7. Richie Porte (AUS/TRE) same time, 8. Mikel Landa (ESP/BAH) s.t., 9. Miguel Angel Lopez (COL/AST) s.t., 10. Daniel Martinez (COL/EF1) s.t.
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