The Slovenian was dropped on the second category climb of Signal d’Uchon and was distanced by his GC rivals with under 20 kilometres to the finish.
The 31-year-old crossed the line more than nine minutes behind stage winner Matej Mohoric and is now 9:11 off in the GC rankings after starting the day only 1:48 in arrears.
Roglič’s struggles on the Signal d’Urchon have all but ended his GC aspirations as he struggled to match the pace with the peloton on the 18 per cent slopes as Richard Carapaz put in two significant attacks.
It has been a tough few days for Roglič who suffered a heavy crash on stage three before losing further time during the stage five time trial.
"It was such a bad crash. He’s in a lot of pain," his team director Merijn Zeeman said after the finish. "He cannot sit normally on the saddle because he also hit his butt on the ground. He’s in a difficult situation.
"It’s just a complete lack of energy to follow. Today that was the case. We are definitely not worried. We just look for chances and see what kind of opportunities there are. Today also the UAE team had a very hard day, they had to follow.
"Pogacar is by far the best but that doesn’t mean the race is over. So we continue fighting and looking for opportunities."
Wout van Aert lies second overall currently for the Jumbo-Visma squad, with Jonas Vingegaard also impressive so far to sit in 11th overall. With Roglič coming in as the sole leader for the squad, it may be a case of those riders and others picking up the pieces, or perhaps Roglič himself if he can recover to near his best.
"We will have to make a plan for that," Zeeman said when asked what Roglič’s approach would be for the rest of the race.
"If he wants to have a chance in this race he needs somehow to recover and that’s something we’ll discuss after the stage with him."
Zeeman was then asked if the Tour de France runner-up from 2020 would abandon the race.
"Too early to say," he said. " We need to discuss it with him first."
The Tour de France continues with the first mountain stage of the race with the Col de la Colombiere the final climb of the day before a descent in Grand Bornand. Watch the race from 20:30 AEST on SBS and SBS OnDemand, with the racing commencing on the SKODA Tour Tracker from 21:00 AEST.