Vonn, the 2010 Olympic champion who on Friday became the oldest ever winner of a World Cup race at the age of 41, went top of the timesheets again after starting 11th, but her celebrations were short-lived.
Aicher, the next skier down the Swiss resort's sparkling Corviglia piste, went 0.24 of a second faster with a time of one minute 30.50 seconds.
It was a third World Cup victory, and second in downhill, for the Swedish-born 22-year-old all-rounder.
"It was a bit more bumpy than yesterday so you felt it," said Aicher, who was fifth on Friday. "My coach always tells me if it's bumpy you have to push even more so I just tried to do that."
Italy's 2018 Olympic downhill champion Sofia Goggia, the ninth starter and a big hope for her home Milano-Cortina Winter Olympics in February, ended up third after Vonn beat her time by 0.05.
Vonn's US teammate Breezy Johnson, the reigning world champion making her 100th World Cup start, finished fourth and 0.40 off the pace.
Vonn, who managed to correct a loss of balance on her run, stayed top of the downhill standings with 180 points from a possible 200.
"I think I skied pretty well but I was a little bit out of balance today," said the American, who felt she had held something back.
"I felt good on the top part of the course but I think yesterday was so emotional, it took a lot of energy and I didn't sleep that great. Hopefully tonight I can get a little bit recharged and ski better tomorrow."
St. Moritz hosts a Super-G on Sunday with Vonn set to be joined on the start list by teammate Mikaela Shiffrin in a race featuring the two most successful women's World Cup skiers of all time.
Shiffrin, winner of a record 104 races, has also made an impressive start to the season with three successive slalom victories.
"I'm really happy with second place but as someone that always wants to get better, I know I can be better," added Vonn.