Lotte Kopecky's bid to catch Haugset failed after a long battle as the Belgian finished one minute and 24 seconds behind the Uno-X Mobility rider. Marianne Vos of the Netherlands crossed the line third in Poligny.
Haugset, 27, secured an overall lead of two minutes and 22 seconds over Kimberly Le Court of Mauritius.
"I never thought it was possible ... it's unreal," said Haugset, who also became the first Norwegian to wear the yellow jersey in the Tour de France Femmes.
"I thought (Kopecky) would catch me. I thought, should I drop down to her? Because second is good... but I thought of everyone cheering from home and I had to give it all."
As the race moved into the hills for the first time, many riders went down in a crash during the category one-climb to Col de la Faucille, including reigning world champion Magdeleine Vallieres and former Tour de France winner Demi Vollering.
Everyone got back on their bikes immediately, and the peloton did not face any breakaway attempts for the rest of the 11.4-km ascent.
Haugset launches solo attack
During the climb to Col de la Savine, Haugset pulled ahead of the bunch. Kopecky pursued her shortly after the halfway mark in the 156.5-km ride, but the Norwegian stayed ahead as the race crossed into France.
Wiebes, riding in yellow, was trailing Haugset by 13 minutes going into the last 20km. Le Court and Vollering, second and third coming into the stage, sat with the peloton over two minutes behind the breakaways.
As Haugset battled exhaustion to stay ahead, Kopecky closed in, reducing the gap to 10 seconds going into the last 10km.
But as the finish line drew closer, 27-year-old Haugset found a second wind, pushing through exhaustion as she put Kopecky nearly a minute back with three kms to go.
Even as Kopecky fell behind, Haugset did not sit up early to celebrate as she sped past the finish line.
"I know my boyfriend will be so angry at me for not celebrating, but I could not even lift my arms off the bike," Haugset said with a smile.
