Schifferer, who won at Beaver Creek, in the United States, earlier this month and was second in the first downhill on Bormio's icy Stelvio piste, clocked 2min 1.44sec from the fifth starting position, despite making errors on the upper part of the piste.
After skiing aggressively on the lower half, he had to watch as skier after skier bettered his half-way split time before fading nearer the finish.
"I spent a long time suffering at the bottom because I made a bit of a mess of the first part of the race," he said. "I was convinced Maier would beat me but it seems he had some problems, too. I was more relaxed today than yesterday and that, along with a bit of luck, made the difference."
Another Austrian, Werner Franz, improved on his third-place finish on Monday by clocking 2:01.62 to take second. He has now finished second in six World Cup downhills but has yet to win one. "That doesn't bother me too much as at the moment consistency's the important thing. We're all looking for places in the Olympic team," he said.
Norway's Lasse Kjus took third place in 2:02.10, but was disappointed. "I don't know what I did wrong to lose almost a second in the second half of the race." said the Norwegian, who was leading at the half-way split.
Maier, the revelation of this season's World Cup, missed out on a top- three finish for only the second time in nine consecutive giant slalom, super-G and downhill races. The 25-year-old overall World Cup leader from Flachau, who beat Schifferer to claim his first World Cup downhill victory on Monday, finished fourth in 2:02.19.