Thomas, who has been protecting overall leader Chris Froome from countless attacks througout the Tour, started the stage in fourth overall, 6min 34sec behind his Sky team-mate.
Unable to keep the pace he has maintained so far, the Welshman struggled overnight and finished 22 minutes behind stage winner Vincenzo Nibali (Astana). The result saw Thomas slide to 15th on the leaderboard, sandwiched between Warren Barguil (Giant-Alpecin) and Thibaut Pinot (FDJ), with a deficit of 27min 24sec.
Team Sky was forced to dig deep on the 138km Alpine stage in the face of attacks from kilometre zero. The race split apart on the opening climb of the Col du Chaussy, before a general regrouping in the next valley eventually brought the peloton back together.
Thomas fell into difficulties on the second major climb of the day, the Hors Category Col de la Croix de Fer. Wout Poels ensured that Froome had a Sky jersey around him for almost the entire stage, with the Dutchman riding hard to provide invaluable support for his team leader.
Froome, though, was eventually isolated and had to fend for himself. He crossed the line in third for the day and lost 30 seconds on the road to Nairo Quintana (Movistar), his closest challenger for the GC honours, who seemed considerably more spritely crossing the finish line than Froome.
After the stage, Froome admitted he was happy to come through the test with the yellow jersey intact, but spared a thought for Thomas.
“It was a tough day for the team, and tough for Geraint losing a lot of time. He was feeling empty after doing such a great job to support me up until now. He’s been there every single day and it’s sad he’s lost his fourth place.
“It’s going to be full-on tomorrow up Alpe d’Huez but I’m actually looking forward to it. It’s the most iconic stage of this year’s Tour.
"It’s going to be epic out there. It would be a dream to take the stage win, but I’ll have to keep up with a little Colombian first.” – Chris Froome
Much like Froome, who rode in support of Sky’s Bradley Wiggins as he won the 2012 Tour, and Australia’s Richie Porte, who is set to leave the team to chase his own goals as a grand tour winner, Thomas’s efforts over the first 19 stages have had people tipping the 29 year old as a potential Tour winner.
“I was just empty today,” Thomas said after losing so much time so close to the finish line in Paris. “It was always going to happen and I was hoping it was going to come on Monday but it came today.
“I just didn't have it, and as they say, sometimes you're the hammer and sometimes you're the nail. I was a cheapy little Ikea nail today. Terrible, but there you go. There's only one mountain stage to go.
“It was such a tough start, and when you've got nothing in the legs there's not a lot you can do.”
Poels finished the stage in 16th, 6min 23sec behind Nibali. Thomas was the next best-placed rider from the Sky team, while Porte finished further back, almost half an hour off the pace.
Tonight’s Alpe d’Huez showdown will confirm whether the rest of the peloton’s efforts have been successful in whittling down Froome’s Sky army, or if the team has left enough in reserve to protect its leader on the Tour’s penultimate, thrilling stage.