After a blistering run, Vonn was 1.22 second faster than leader Viktoria Rebensburg of Germany at the final intermediate time but went off-course and just made the next gate shortly before the finish section.
"I had a great run but was much too straight in that banana turn," Vonn said. "Coaches had told me I could approach that turn straight, but at my speed it was just impossible ... It was a little bit of a miscommunication. The line we talked about was too direct."
Vonn had to slow down to get back on the course and lost almost two seconds to trail Rebensburg by 0.57 at the finish.
The American standout had already secured the discipline title before the start of her run. Sole rival Anna Fenninger had to win the race to stand a chance of closing the 94-point gap with Vonn, but the Austrian came fourth.
It was Vonn's 16th career crystal globe and the fourth in super-G. This season, she won four of seven races in the discipline.
Vonn has two races left to earn 53 points and overtake Austrian great Hermann Maier's record of 2,000 World Cup points in one single season.
Vonn is also closing in on the women's best mark of 1,980 points held by Janica Kostelic of Croatia.
"A shame I didn't manage to get there today," said Vonn, who was considering skipping Saturday's slalom and put in extra giant slalom training.
Vonn failed to finish her last three slaloms, while she had an outstanding GS season with her first two wins in the discipline.
"I am not sure to do the slalom and maybe prepare for the GS," Vonn said. "Or I might do the slalom to try to get some points to put pressure off the GS. That decision I will make tomorrow. Let's see how much energy I've left and go from there."
In sunny and warm conditions, Rebensburg finished the Streicher course in 1 minute, 24.54 seconds to beat Julia Mancuso of the United States by 0.18 seconds and Marion Rolland of France by 0.21 to win her first career super-G race.
"It's a matter of self-belief," said Rebensburg, who is favoured to take the giant slalom title on Sunday. "I knew I could do well in super-G as well. It's all about putting in an error-free run at a race. I am excited it happened today."
Mancuso's second place meant the American overtook Fenninger in the super-G standings to finish second behind Vonn.
"It was a lot of fun to race on this kind of (soft) snow," Mancuso said. "You have to ski really well to win. I lost some time on the traverse so I have to figure that out before next year's world championships."
Super-G has been Mancuso's best event this season. She won in Garmisch-Partenkirchen, Germany, last month and finished at least in eighth position at all seven races.
The American said that switching ski brands two years ago has helped her to become more consistent. She won silver in super-G at the world championships in 2011.
"Since I switched, I have been really successful," Mancuso said. "Super-G is a difficult event, you have to nail your inspection. It's really cool to be skiing that fast, it's exciting."
The World Cup finals continue with a team event Friday before the men's and women's technical races over the weekend wrap up the season.