Hirscher, who was third after the opening leg, was fastest in the second run to finish in a combined time of 1 minute, 44.34 seconds. The defending overall champion extended his lead in both the overall and slalom World Cup standings.
Felix Neureuther of Germany came 0.77 back in second, and Kostelic finished 0.91 behind Hirscher. The Croat became the first skier to win the combined event in Kitzbuehel for four straight years.
Stefano Gross of Italy, who led the race after the opening leg, lost speed after a mistake and finished outside of the top 10.
Michael Janyk of North Vancouver, B.C., was the top Canadian in 14th.