Geraint Thomas chased a fierce attack by his Team Ineos teammate Egan Bernal, yet still lost second place overall to the Colombian as the tension in the Tour de France ramped up another notch and the unflappable Julian Alaphilippe again clung on to his overall lead.

Bernal, widely tipped for victory before the Tour began, was finally unleashed by Team Ineos in the thin air on the approach to the 2,642-metre summit of the Col du Galibier as his fellow Colombian Nairo Quintana rode clear on his own to a third career stage win in the Tour.

“It was Geraint’s decision,” Bernal said of his attack. “He asked me to attack to try to move the race and tried to come with me but when he saw the other guys on his wheel he just stayed with them. But I attacked because he asked me to attack.”

Bernal’s first real acceleration of this Tour quickly left the other main contenders in his wake, yet as he opened up a lead Thomas led the pursuit as his 22-year-old teammate crossed the top of the Galibier. When Thomas’s tactics were queried, Bernal said: “We need to gain time on Alaphilippe. I don’t care what happens with G[eraint]. You never know how the other guys are and if you try to do the race hard Alaphilippe can be dropped and it’s on … I think that we did a really good race today.”

Julian Alaphilippe and Geraint Thomas stalked each other for much of Stage 18. Photograph: Tim de Waele/Getty Images

Thomas described his chase as “a little dig”, but there was little doubt his move pulled Ineos’s rivals along in his wake and affected Bernal’s lead. “We wanted a hard pace but unfortunately we ran out of guys, and it didn’t seem quite hard enough so the call was made for Egan to jump,” Thomas said of the long haul to the top of the final climb. “Hopefully that would kick it off – but it didn’t really.”

There is no question, however, that if Thomas had not given chase Bernal’s advantage at the finish might have been greater than 32sec and he might also have taken more time from a struggling Alaphilippe. “I had a little dig to just see what would happen,” Thomas said. “They obviously followed me over the top [of the Galibier] but I think it was a good day for Egan, gaining some time.”

Later, the Team Ineos principal Dave Brailsford spoke to French broadcasters about the leadership situation, saying: “We will discuss this between ourselves – we are going to decide tonight. For me, there is no difference of level between the two. They are two good climbers.”

Bernal now leads the defending champion Thomas by 5sec in the overall standings but crucially he has also overtaken Thibaut Pinot and Steven Kruijswijk, who both fought hard to keep pace with the accelerations by Thomas towards the top of the Galibier. The Colombian’s show of strength has justified the growing belief that he, rather than Thomas, has been Ineos’s chosen son throughout this race.

All that stands in Bernal’s path to yellow now is Alaphilippe, who again stunned his rivals by erasing his deficit at the top of the Galibier with a balletic descent to the finish in Valloire. Dropped in the final moments of the climb, Alaphilippe plummeted through the hairpins, brushing parked camper vans and cutting corners. Halfway down the 19km descent he caught the five-man group of Thomas, Rigoberto Urán, Pinot, Emanuel Buchmann and Kruijswijk and sped past them.

“I gave everything on the climb and I took some risks on the descent, but I absolutely wanted to defend the jersey,” the Frenchman said. “I was on my limit but the gap was not too big, so I just gave full gas to come back. I gave everything. I knew that it would be a really hard day and that everyone wanted to push me to my limits but I’m ready for tomorrow now.” he said.