Michal Krcmar of the Czech Republic won the silver medal and Dominik Windisch of Italy the bronze.
Peiffer and Krcmar were the only two athletes not to miss the target on a windy, freezing night that made both shooting and skiing difficult.
Race favourites Martin Fourcade of France and Norwegian Johannes Thingnes Boe both left themselves with a mountain to climb by missing three of their first five shots.
World Cup leader Fourcade, a double gold medallist at the Sochi Games, had to content himself with eighth place, while Boe finished a disappointing 31st.
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With temperatures well below freezing and a bitterly cold, howling wind whipping up the snow on exposed parts of the course, many of the competitors struggled to find their range, but Peiffer seemed unperturbed.
Similar to his compatriot Laura Dahlmeier, who won the women's event at the same venue 24 hours earlier, the 30-year-old Peiffer powered his way around the course and was a picture of composure on the shooting range.
Though Krcmar matched his shooting prowess, Peiffer was slightly faster across the snow and finished 4.4 seconds ahead of his rival to take the gold medal, with Windisch of Italy a further 3.3 seconds behind.
(Editing by Clare Fallon)
