Ligety trailed the Frenchman after the slalom part of the race by 1.22 seconds but came on strong in the downhill portion to win at Wengen, Switzerland, with a combined time of 2 minutes, 44.74, a scant 0.22 seconds ahead of Pinturault.
Natko Zrncic-Dim of Croatia took third place and Aksel-Lund Svindal of Norway, the overall men's World Cup points leader, placed fourth with a 2:46.22 that included a blistering downhill time of 1:51.96.
Ligety, who was timed at 1:53.58 in the downhill, said the downhill course didn't have the best snow conditions but the sunlight was optimal for his style.
"I feel lucky that we had good light. In downhill, if I don't feel confident enough to go hard I let myself go slow so I can see where I'm going," Ligety said.
"I was lucky in the morning running first [in the slalom] because I got a super smooth course and that helped me relax and stay enough ahead of the downhill guys despite not skiing a fantastic run."