Birnbacher had to do it the hard way, fighting back to recoup some lost ground after one wayward effort on the third round of shooting, before holding off Anton Shipulin and Martin Fourcade to take the win in 38.45.7 minutes.
Russian Shipulin was second, just 0.1 of a second back with Frenchman Fourcade – who like the whole of the top three had a solitary missed shot – also less than a second shy of Birnbacher.
Fredrik Lindstrom and Michal Slesingr completed the top five as Birnbacher enjoyed a day to remember to reduce the overall World Cup lead of Fourcade.
The German now trails Fourcade by 52 points in third place with Emil Hegle Svendsen, who endured a poor day in Italy finishing 14th, in second, 27 points adrift.
France won the women's 4 x 6km relay. Belarus were second, 2.5 seconds behind, with Russia third.
The women's 12.5km mass start is on Sunday.