Defago was clocked in 2 minutes, 31.98 seconds, a fifth of a second ahead of Miller, CNN reported.
Miller's run at Wengen gave him his fourth top-three finish this year. He has been on the podium after 16 downhills in his career, four times at Wengen.
"I've shown that I can win on this course, but it was tough this year with only two training runs," Miller said. "I was happy with going out and putting out a hard race."