The Bayern Munich goalkeeper's first appearance since suffering a foot injury in September had looked in jeopardy after heavy rain hit Klagenfurt shortly before kick-off.
After officials undertook three separate pitch inspections, the game finally started an hour and 45 minutes later than originally scheduled.
However, that uncertainty did little to disrupt Mesut Ozil, who took advantage of an early error from Austria goalkeeper Jorg Siebenhandl to give Joachim Low's side an 11th-minute lead.
Yet Austria were a much tougher proposition in the second period, with Martin Hinteregger and Alessandro Schopf scoring fine goals to seal a memorable triumph over their neighbours and stretch their winning streak to an impressive seven games.
After such a lengthy delay, it was hardly surprising that the game started in disjointed fashion with neither side able to fashion anything resembling a chance.
That changed after 11 minutes, though, thanks to Siebenhandl’s mistake. The Sturm Graz keeper inexplicably clipped his attempted clearance straight to Ozil, who took a touch before curling a left-footed strike into the far corner.
Germany really should have doubled their advantage 10 minutes later, but Julian Brandt's low effort after a flowing move was diverted agonisingly past the far post by the legs of Siebenhandl.
Shortly before half-time, Neuer demonstrated that his lay-off had done nothing to diminish his agility. Florian Grillitsch must have thought his low strike was creeping in at the near post, only for the 32-year-old to get down sharply and push the ball past the post.
The hosts started the second period with the type of intensity that was lacking in their tepid first-half display and were duly rewarded with a fine equaliser after 53 minutes.
David Alaba's deep corner from Austria’s right was met at the back post by the unmarked Hinteregger, who flashed a fierce, first-time volley from a tight angle beyond the helpless Neuer.
Marko Arnautovic was denied just moments later by Neuer’s outstretched hand as Austria pinned their illustrious opponents against the ropes.
Their deserved winner arrived in the 69th minute when Schopf met Stefan Lainer's back-post knockdown, the Schalke midfielder sweeping a first-time effort into the net to complete the turnaround.
Low made a raft of substitutions in the closing stages, but none of the changes had the desired impact as Germany’s World Cup preparations suffered an unlikely setback.