Joachim Low's side made it two wins from as many World Cup qualifying matches, but endured a nervy first half as the hosts searched for an equaliser
Marco Reus gave the visitors the lead on the stroke of half time, and Mesut Ozil made it two from the penalty shot shortly after the break. However, Zlatko Junuzovic ensured a nervy ending to match, but die Nationalmannschaft had done enough.
Germany may have gone into the break a goal to the good, but in truth either side could, and perhaps should have taken the lead long before the deadlock was eventually broken.
Just a couple of minutes were on the clock when Mats Hummels sprayed a wayward pass to Julian Baumgartlinger, who sent an inch-perfect ball to Martin Harnik. The Stuttgart star was preparing himself to apply the finish, but Holger Badstuber got across to make a fantastic tackle and save his defensive partner's blushes.
Seconds later, a calamitous defensive error almost led to a goal at the other end as Robert Almer sliced a clearance with Miroslav Klose lurking, but the ball bounced kindly out of play, and away from the 34-year-old.
Neither side had settled, and another lapse at the back presented Harnik with a chance that he screwed wide, before Klose failed to capitalise on a shoddy clearance that came straight to him, with Almer atoning for his earlier moment.
Harnik and Andreas Ivanschitz had driven a long-range effort apiece wide, before Germany finally started to click. Toni Kroos had a couple of shots from distance which failed to break the deadlock, and Thomas Muller brilliantly met Mesut Ozil's free kick, only for Almer to get down low and make an excellent save.
Austria had appeals for a penalty turned down when Badstuber appeared to fell Harnik after the Stuttgart man reacted quickly to a quickly-taken throw, and a poor clearance from Neuer almost teed up Baumgartlinger, but the visitors were about to strike.
Miroslav Klose collected the ball with his back to goal and teased a cute ball in to Reus, who coolly cut inside Gyorgy Garics and passed the ball into the bottom corner.
German nerves were finally settled, and they began the second half in the same manner they ended the first. Toni Kroos attempted to cut the ball back from the byeline to Muller, only for Veli Kavlak to clatter into the Bayern attacker, and Ozil made no mistake from the spot.
The Real Madrid playmaker almost created another instantly, but Mario Gotze, who had expertly taken the ball around Almer saw his effort rightly disallowed. Had it counted, the contest would have been over.
However, the two-goal lead lasted for just a matter of minutes. Marko Arnautovic raced down the right wing, left Marcel Schmelzer for dead and delivered a delicious ball into the middle of the park, and Junuzovic darted in front of the static Hummels and diverted it home.
Germany immediately set about trying to get a third, and Philipp Lahm almost proved to be the difference, delivery two crosses, one of which was almost diverted past Almer by an Austrian, the other found Muller, who could only sky an effort miles over the bar when he should have done far better.
Austria's potent front line was still proving to be a threat to the visitors, though, and Arnautovic soon exposed Schmelzer's deficiencies at left-back once more, but could not pick out a team-mate with his cross.
The hosts were almost gifted an equaliser with just under 20 minutes to play when Lahm's back-pass went straight to Guido Burgstaller, but Neuer was on hand to rush off his line and and claim the ball, sparing the blushes of his skipper.
Lahm soon made himself a hero though when he cleared Baumgartlinger's header off the line, before Arnautovic miscued an effort a matter of inches from goal after being set up by a tantalising ball from the left wing, but that signalled the end of the Austrian assault on Germany's goal.
The visitors were able to pass the game out and secure a repeat of the result they earned in Vienna in qualifying for Euro 2012.