Triple world champion Ligety, who secured the giant slalom World Cup last weekend, beat overall title winner Marcel Hirscher of Austria by 0.37 seconds to take his sixth win of the season in the discipline.
His win came an hour after teenage team mate Mikaela Shiffrin had taken the women's slalom World Cup with victory in the event's final race at this Swiss resort.
Frenchman Alexis Pinturault was third in the men's race on the Silvano Beltrametti course, his third podium place in succession in giant slalom.
Hirscher's result allowed him to finally enjoy his second overall title after securing it on Thursday, the day his team mate Klaus Kroell crashed and was injured in a super-G that was eventually called off.
"I always said I would not feel the rightful winner of the World Cup before I had the globe in my hands but with what I did today I can really consider I won it," said the Austrian, the first skier to retain the overall title since his compatriot Stefan Eberharter 10 years ago.
"I needed to score more big points to really feel like the winner of the overall globe and it has nothing to do with the cancellations here, it's between me and myself," he added.
The Lenzerheide finals were tarnished by the cancellations of both speed events, decisions which quashed the chances of Hirscher's main rival this season, Norwegian Aksel Lund Svindal.
Hirscher, who has had six World Cup victories, a slalom world title and 17 podium places this season, will be the favourite in the final race of the season, Sunday's slalom on the same course.
The Austrian said he expected an even tougher fight from Ligety next season.
"Just because I won the World Cup twice I won't automatically win it a third time," he said. "If Ted stops making mistakes in slaloms, he'll be a serious contender. He's extremely strong."
Ligety said his opponents kept him on his mettle.
"It's been a constantly exciting season of great fights with Marcel and Pinturault. I'm proud of what I've done but I'm also looking ahead because I know that if I train just a little less hard, they'll beat me," he said.
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- Marcel Hirscher