Miroslav Klose scored the only goal of the game in the 34th minute as Germany weathered early and late storms and rode their luck after Jerome Boateng was sent off on his debut in the 69th minute.
But Joachim Low's side held on to open up an unassailable four-point lead at the top of Group Four with one game remaining, leaving Guus Hiddink's Russia with the consolation of a place in the play-offs.
Aleksandr Kerzhakov had the first chance of the game in the sixth minute when he turned well on the edge of the penalty area and shot straight at Germany goalkeeper Rene Adler.
The Russia striker was heavily involved in the early action and his eighth-minute volley wide of the post was the next warning to Germany that they were in for a tough night at the Luzhniki Stadium.
But the visitors held firm early on and a good combination between Lukas Podolski and Mesut Ozil carved open the Russia defence for the first time with the former's goal-bound shot blocked by the outstretched leg of Sergei Ignaschevich.
Andrey Arshavin then played a neat ball into the path of Vladimir Bystrov, who was left with only Adler to beat, but the Germany number one made the first of numerous crucial saves to deny him with his legs.
Low's side went ahead in the 34th minute with Podolski and Ozil again linking well. The latter pulled the ball back from the by-line to Klose, who managed to dig the ball out from behind his stride and direct it inside the near post.
Russia now needed to score two to move into pole position for World Cup qualification and it was no surprise that they laid siege to Adler's goal in the second half.
Kerzhakov was through again with just Adler to beat in the 53rd minute, but this time he was unable to fully control the ball.
He did, however, manage to lay it off for Arshavin, whose 18-yard shot drew a fine save out of Adler with Kerzhakov unable to react well enough to convert the rebound.
Adler denied Arshavin again moments later as Russia increased the pressure and the Germany goalkeeper was somewhat fortunate to see his save from Yury Zhirkov trickle just wide of the post and not inside it.
Germany had their backs to the wall and Boateng, making his debut, was sent off for a second yellow card in the 69th minute for a foul on Vladimir Bystrov.
But Russia were unable to take advantage of their extra man on the field, although they were unfortunate not to be given a penalty late on.
The contact Michael Ballack made on Arshavin was innocuous enough, and referee Massimo Busacca was right to wave play on, but the Russians will have felt aggrieved when the Swiss official again opted not to point to the spot moments later after Arne Friedrich fouled Bystrov.