Hampered by a lingering knee injury, the Croatian had not won a slalom race this season but the 33-year-old broke his duck in style to earn his 26th World Cup victory after clear first-leg leader Alexis Pinturault messed up his second run.
The 33-year-old clocked a combined time of one minute 45.81 seconds to top the podium ahead of Marcel Hirscher who fought back from a poor morning run to claim second place and secure the World Cup title in the discipline.
Austrian Hirscher, who was 0.19 seconds adrift, secured the crystal globe he narrowly lost to Swede Andre Myrher last year after his only rival left in contention, Germany's Felix Neureuther, straddled a gate in the morning run.
Hirscher also strengthened his overall World Cup lead as closest opponent Aksel Lund Svindal of Norway now trails him by 149 points before the Lenzerheide finals next week.
"It's of course nice to have clinched that globe today but my main goal this morning was to achieve another strong race here," said Hirscher.
"I gave my all this afternoon as I only care for big points when I race and I wanted to try as hard as possible. It's really nice to be second and score crucial points before the Lenzerheide finals."
Another experienced skier, Ausria's Mario Matt, 33, took third spot, 0.34 behind Kostelic.
"I'm very relieved because this race was very important for me. It's a great feeling for it's not easy to stay at the top level, the competition is very dense," Kostelic said.
"This victory means a lot to me, especially since I have been informed by my doctors that my meniscus is badly injured again. I'll need surgery within a few weeks so I told myself that I had nothing to lose."
Kostelic was a little lucky that young Frenchman Pinturault overdid it in the second run and straddled a gate as he was leading the rest of the field by one and a half seconds.
"I knew that Alexis had to make a big mistake for me to win. So I was really pushing today but I was focused on that," Kostelic said.