Kroell crossed the finish line in 2 minutes, 4.22 second with Miller hot on his tail in 2:04.23 and Didier Cuche of Switzerland in third place in 2:04.26.
Cuche remained first in the overall downhill points standings and Austria chalked up its first downhill victory of the season.
Miller said afterward he felt he lost the race at the very end. "There's so many places where 0.01 can come or go," Miller said. "I didn't really have a great reach for the finish line, which I always try to do well."
Snow conditions were on the wet side, which Miller said made it tougher for the competitors to control their skis.
Friday's race was a make-up for the event in Val Gardena, Italy, which was canceled due to high winds, and was the first of two downhills scheduled in Chamonix this weekend.