Ligety was in third place after the opening run, but he skied out on the second leg.
"End of the season, my motivation is just totally sapped," said Ligety, of Park City, Utah, who wrapped up his fifth World Cup GS title last weekend. "I'm beat up physically and pretty 'over it' mentally."
Jitloff earned his fifth national title, including a second consecutive in giant slalom. He also won that event in 2008 and 2009, along with a combined title in 2009.
Jitloff, who grew up in Reno, Nev., and used to go skiing in Squaw Valley as a kid, finished Friday's two runs in 2 minutes, 22.45 seconds.
He was fastest in the first leg, then held onto his lead by being second-fastest in the second leg.
Jitloff was 15th behind Ligety in the Olympic giant slalom last month.
"He's one of the faster guys in the world, for sure," Ligety said. "He's on his home hill, so of course he was going to be tough to beat."
Heading into the second run, Jitloff explained, "I just said, 'I'm going to take it pretty easy in there.' I heard that Ted had gone out. ... It was sketchy in there for a second, but I kept it solid, I kept it safe. And then when I got to the bottom here, I did charge."
Brennan Rubie was next in 2:24.06, turning in the fastest second leg to rise from sixth place. Jared Goldberg finished third.