The Frenchman (6:00:54) was able to come around Austrian Gregor Mühlberger, who opened the final sprint, and beat him by a whisker to take his tenth victory of the season.
Italy’s Alessandro De Marchi came in 22 seconds later to take third.
Julian Alaphilippe said he was always hungry for success and every victory was important for him and his team.
“To win in the Dauphine in my first race in France is a really special feeling. I’m really happy after a hard day in the break, with only three guys.
“I know my mate from the breakaway, from Bora. He’s really strong and I know he’s explosive.”
The Deceuninck-QuickStep rider said he had to be careful and did not want to start his sprint in the finish too early due to a headwind.
“So I passed him (Mühlberger) in the last moment,” said Alaphilippe.
He added that he was in good form and that he would continue to work until the Tour de France.
“But I want to enjoy this win. It’s a really beautiful victory.”
Britain’s Adam Yates (23:35:04) finished safely in the peloton to retain the lead in the overall standings. Belgium’s Dylan Teuns (+0:00:04) lies second, followed by America’s Tejay van Garderen (+0:00:06).
More results can be viewed below.
Stage six results
1. Julian Alaphilippe (Fra) Deceuninck-QuickStep 6:00:54
2. Gregor Mühlberger (Aut) Bora-Hansgrohe
3. Alessandro De Marchi (Ita) CCC +0:00:22
4. Wout Poels (Ned) Team Ineos +0:06:10
5. Gorka Izagirre Insausti (Spa) Astana Pro Team
6. Jakob Fuglsang (Den) Astana Pro Team
7. Jack Haig (Aus) Mitchelton-Scott
8. Adam Yates (GBr) Mitchelton-Scott
9. Nairo Quintana (Col) Movistar Team
10. Alexey Lutsensko (Kaz) Astana Pro Team
87. Daryl Impey (RSA) Mitchelton-Scott +0:17:13
100. Stefan De Bod (RSA) Dimension Data +0:18:26
107. Jaco Venter (RSA) Dimension Data +0:18:36
1. Adam Yates (GBr) Mitchelton-Scott 23:35:04
2. Dylan Teuns (Bel) Bahrain-Merida +0:00:04
3. Tejay van Garderen (USA) EF Education First +0:00:06
4. Jakob Fuglsang (Den) Astana Pro Team +0:00:07
5. Steven Kruijswijk (Ned) Team Jumbo-Visma +0:00:24
6. Thibaut Pinot (Fra) Groupama-FDJ +0:00:25
7. Emanuel Buchmann (Ger) Bora-Hansgrohe +0:00:26
8. Alexey Lutsenko (Kaz) Astana Pro Team +0:00:30
9. Nairo Quintana (Col) Movistar Team +0:00:40
10. Wout Poels (Ned) Team Ineos
77. Stefan De Bod (RSA) Dimension Data +0:29:09
79. Daryl Impey (RSA) Mitchelton-Scott +0:29:25
129. Jaco Venter (RSA) Dimension Data +0:52:58