The 27-year-old French star attacked near the top of the Côte de Mutigny, the last of four climbs on the 215km course, and soloed the final 15km to an impressive stage victory. Michael Matthews (Sunweb) and Jasper Stuyven (Trek-Segafredo) led the bunch home, 26 seconds in arrears.
Alaphilippe, who won a stage and the climber’s jersey at the Criterium du Dauphine just before the start of the Tour, has been in good form all year and the final ramp suited his strengths.
He took his opportunity as the bunch was about to reel in Tim Wellens (Lotto Soudal), the last remaining rider from the day’s early break, and the rest of the favourites had no answer to his acceleration that reminded of his victory at La Flèche Wallonne.
At that stage, overall leader Mike Teunissen had already been left behind and the Deceuninck-Quick-Step rider knew the yellow jersey was up for grabs if he could win by a decent margin.
“I’m speechless. 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,” Alaphilippe told reporters afterwards.
“I heard I was 30 or 40 seconds ahead. It’s difficult to meet the expectations of being the favourite but I made it. I’m delighted.”
The breakaway of the day consisted of Wellens, Stephane Rossetto (Cofidis), Yoann Offredo (Wanty-Gobert), Anthony Delaplace (Arkea-Samsic) and Paul Ourselin (Total Direct Energie), who achieved a maximum lead of 6:15 with 133km to go. Wellens attacked 47km out as they headed towards the first of four climbs, the Nanteuil-la-Forêt, to take the lone lead.
Behind, his fellow escapees were caught by the bunch as he hung on to a 1:14 lead at the bottom of the penultimate climb, the Côte de Champillon. This was reduced to 56 seconds at the bottom of the Mutigny.