The 27-year-old Deceuninck-Quick-Step rider won the 215km stage, which started in Binche, in a time of 4:40:29.
Michael Matthews (Team Sunweb) claimed second, with Jasper Stuyven (Trek-Segafredo) third.
“Third is good result. It means that I’m good. Then again, nobody will talk about it in a few days,” said Stuyven.
“Alaphilippe was clearly the strongest, staying ahead despite the wind. I didn’t see him go. I was behind on that climb.”
The stage winner also took the yellow jersey, with Wout van Aert (Team Jumbo-Visma) second overall and Steven Kruijswijk (Team Jumbo-Visma) third.
View more results below.
1. Julian Alaphilippe (Fra) Deceuninck-QuickStep 4:40:29
2. Michael Matthews (Aus) Team Sunweb 4:40:55
3. Jasper Stuyven (Bel) Trek-Segafredo 4:40:55
4. Greg Van Avermaet (Bel) CCC Team 4:40:55
5. Peter Sagan (Svk) Bora-Hansgrohe 4:40:55
6. Matteo Trentin (Ita) Mitchelton-Scott 4:40:55
7. Sonny Colbrelli (Ita) Bahrain-Merida 4:40:55
8. Xandro Meurisse (Bel) Wanty-Gobert 4:40:55
9. Wout Van Aert (Bel) Team Jumbo-Visma 4:40:55
10. Thibaut Pinot (Fra) Groupama-FDJ 4:40:55
54. Daryl Impey (RSA) Mitchelton-Scott +0:00:31
106. Reinardt Janse Van Rensburg (RSA) Dimension Data +0:09:32
1. Julian Alaphilippe (Fra) Deceuninck-QuickStep 9:32:19
2. Wout Van Aert (Bel) Team Jumbo-Visma 9:32:39
3. Steven Kruijswijk (Ned) Team Jumbo-Visma 9:32:44
4. George Bennett (NZl) Team Jumbo-Visma 9:32:44
5. Michael Matthews (Aus) Team Sunweb 9:32:59
6. Egan Bernal (Col) Team Ineos 9:32:59
7. Geraint Thomas (GBr) Team Ineos 9:33:04
8. Enric Mas (Spa) Deceuninck-QuickStep 9:33:05
9. Greg Van Avermaet (Bel) CCC Team 9:33:10
10. Wilco Kelderman (Ned) Team Sunweb 9:33:10
24. Daryl Impey (RSA) Mitchelton-Scott +0:01:06
103. Reinardt Janse Van Rensburg (RSA) Dimension Data +0:10:55