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The American will win the discipline title if he finishes ahead of Marcel Hirscher of Austria, who is 0.60 behind Ligety in fourth place.
On a softened Podkoren course because of mild weather, Ligety went down in 1 minute, 22.16 seconds to lead Alexis Pinturault of France by 0.20 and Felix Neureuther of Germany by 0.22.
"The snow is really soft," Ligety said. "It's hard to keep your edge in the snow well. It didn't feel good at all. This is a very difficult course set, especially for how the snow is running. It was tough to have a good feeling, so I am happy with where I am sitting."
Ligety won the World Cup giant slalom in 2008 and 2010-11. He also successfully defended his GS title at the world championships last month.
The course Saturday was set by Austrian slalom coach Michael Pircher. He designed numerous sharp turns, an unusual feature for a GS and one that didn't benefit Hirscher.
"I don't know why it didn't go better," said Hirscher, who beat Ligety for the GS title last season. "My feeling was OK, but obviously it wasn't good. It's hard to tell (why), it's a mystery to me."
The course was further affected by rain, making conditions for the second run even worse. Ligety, however, isn't worried about having to start as the 30th and last racer.
"If you're starting last in the second run it means you're winning, so I'd rather be there than not there," said Ligety, who has won in Kranjska Gora four times and been on the podium every year since 2008.
Aksel Lund Svindal of Norway, who is competing with Hirscher for the overall title, was 0.99 back in fifth place. Benjamin Raich trailed Ligety by 1.33 in sixth. The Austrian has also won four times in Kranjska Gora.
The last GS of the season takes place next Saturday during the World Cup finals in Lenzerheide, Switzerland.
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