The 27-year-old had posted the fastest time in the first leg and did not disappoint in the second run, beating Loic Meillard of Switzerland by 1.13 seconds.
Haugan's compatriot Atle Lie McGrath finished third, 1.26sec adrift of the winner.
"I'm super stoked to have my team-mate on the podium," said Haugan.
"Me and Atle had a talk yesterday, a little bit about the mental stuff with ski racing and it's really cool to see how we both have learned so much the last years and really stepped it up."
McGrath was impressed by his compatriot's performance.
"What Timon did in that second run was just incredible. He smoked us all which was so much fun," said McGrath.
"Always when a Norwegian wins it's great -- two Norwegians on the podium is also really good.
"We are keeping the slalom streak alive of being on the podium every race."
France's Clement Noel, winner of the first two slaloms of the campaign, skied as if he is still feeling the right ankle injury that ruled him out of the previous race in Val d'Isere.
The Olympic champion was third after the first leg but dropped to sixth after the two runs.
Switzerland's Marco Odermatt does not compete in the slalom but still tops the overall World Cup standings after an impressive weekend's work, emerging triumphant in both the downhill at Val Gardena and then the giant slalom in Alta Badia on Sunday.
He holds a 71-point lead over Haugan and McGrath's teammate Henrik Kristoffersen, who was fourth in the slalom.
The men stay in Italy for the next round of World Cup races, a downhill and then a super-G in Bormio next Saturday and Sunday.
