American Vonn, whose 77 career World Cup race triumphs are a women's all-time record and trail only Swedish great Ingemar Stenmark's mark of 86 wins, clocked one minute 48.29 seconds.
That left her 0.15 seconds behind Czech Ester Ledecka and 0.54 seconds ahead of Liechtenstein's Tina Weirather, who had the fastest time in the first training run.
The Canadian resort west of Calgary will host the start of the women's speed season with downhill races on Friday and Saturday and a Super-G on Sunday.
"It was a solid training run but I can definitely clean up a few sections for tomorrow," Vonn told reporters. "But I'm confident I feel good. Today was solid and a good sign for the weekend."
Vonn has won 14 downhill races in Lake Louise and four Super-Gs.
Vonn was much faster than her first training run on Tuesday when her time of 1:51.71 was the eighth quickest.
She was unable to get a training run in on Wednesday as soft snow forced the cancellation of the session but will take plenty of confidence into Friday's race knowing exactly where she needs to make adjustments.
"I was just a little too straight up top everyone seemed faster than me up top I just need to stay out of the soft snow," said Vonn. "It always feels the same here I love it here."
(Reporting by Steve Keating,; Writing by Frank Pingue, editing by Ed Osmond)
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