Alaphilippe took yellow off the shoulders of Mike Teunissen as he attacked on the final categorised climb of Monday’s 215km stage from Binche to Epernay, while the steep finish in the capital of Champagne country was enough to see Thomas lose the wheel of Team Ineos colleague Bernal.
A five-second gap between the two sees Thomas end the day seventh in the nascent general classification standings, 45 seconds down on yellow with Bernal in sixth, 40 seconds off Alaphilippe.
Victory for the 2018 King of the Mountains was little surprise on a Classics-style stage which seemed ideally suited to his explosive style.
“He may have designed today’s stage himself,” Mitchelton-Scott sporting director Matt White joked this morning.
“It’s like the Amstel Gold Race in a French vineyard.”
Even so, Alaphilippe had to execute in order to take his first career yellow jersey and he did so in style.
“I’m speechless,” the 27-year-old said. “I don’t realise what’s happening to me. I knew this stage suited me.
“I managed to avoid any pitfalls and crashes. I felt good so I accelerated in the Mutigny climb but I didn’t think I’d go alone.
“I gave everything. I heard I was 30 or 40 seconds ahead. It’s difficult to meet the expectations being the favourite. I made it. I’m delighted.”
Little happened on the long road south from Belgium, virtually flat until the final 45 kilometres when the riders hit the lumps of Champagne country.
The peloton was bearing down on Lotto-Soudal’s Tim Wellens, the last survivor of the day’s breakaway, as they hit the 12 per cent inclines of the Mutigny inside the last 20 kilometres.
As the summit came into view Alaphilippe launched his move, cresting the summit on Wellens’ wheel before bursting clear, at the same moment as Jumbo-Visma’s Teunissen was being jettisoned out the back.
Alaphilippe’s advantage was already 50 seconds by the time he reached the foot of the descent.
There were still challenges to come – the uncategorised Cote du Mont Bernon inside the final five kilometres and then the eight per cent gradients of the finish itself – but Alaphilippe always looked in control as he powered clear.
He crossed the line some 26 seconds ahead of a much-reduced pack, led home by Team Sunweb’s Michael Matthews, but the more notable gaps appeared behind as Thomas lost the wheel of Bernal in the finale.
The Welshman will be grateful that Groupama-FDJ’s Thibaut Pinot was the only other general classification hopeful in front of him, and though five seconds is a tiny margin, it could prove a significant moment as the co-leaders vie for supremacy within Team Ineos.
Britain’s Mitchelton-Scott rider Adam Yates finished 25th in the same time as Thomas alongside a host of other general classification contenders, including Jumbo Visma’s Steven Kruijswijk, AG2R La Mondiale’s Romain Bardet and the 2014 champion, Bahrain Merida’s Vincenzo Nibali.