However the German goalkeeper appears to have won his fitness battle to play at the World Cup, and will be leading his side into the tournament as defending champions.
"For the moment everything is on plan for Manuel Neuer".
Loew declined to comment when a poll by national broadcaster ZDF showed the majority of German fans would rather see Barcelona goalkeeper Marc-Andre Ter Stegen than Neuer play at the World Cup.
"I'll talk to him tonight and if everything is okay, he'll play against Austria". "He hasn't had problems in the match or in training this week".
Austria have failed to qualify for the World Cup, while Germany face Saudi Arabia on Friday in their final warm-up before playing Mexico on June 17 at Russian Federation 2018.
Germany will face Mexico, Sweden and South Korea in Group F.
Mats Hummels and Thomas Mueller, who are rested, are also being left behind in Eppan by Loew, but for the rest of the 27-man squad this is their last chance to win a place on the plane to Russian Federation.
Germany started brightly and took the lead after kist 11 minutes, with Arsenal's Mesut Ozil capitalising on a poor clearance from goalkeeper Jörg Siebenhandl and producing a fine finish. He was only beaten by a Thomas Mueller penalty and a Julian Draxler goal.
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Germany almost doubled its lead in the 20th when Julian Brandt broke through after a quick combination between Joshua Kimmich and debutant Nils Petersen, but the Leverkusen midfielder had his low shot saved by Siebenhandl.
At the other end, Neuer made his first save on 16 minutes to deny attacking midfielder Schoepf.
Zulj saw another effort roll inches past the post before Schopf beat Neuer for the second time after 69 minutes, converting a cut-back from Stefan Lainer from close range. "We didn't execute many things we had planned", Loew said.
A frustrated Kimmich said: "There are not a lot of positive things to say after a game like that". We won't fool ourselves.
Saturday's game was subject to a long pre-match delay due to heavy rain, with Low left annoyed by his side's poor performance against Austria, who recorded a seventh straight win despite failing to qualify for the World Cup.
After 259 days out injured, Neuer pulled off a string of saves in an impressive first-half display, but had little chance to stop Austria's goals after Germany's defence leaked badly in the second half.
After officials undertook three separate pitch inspections, the game finally started an hour and 45 minutes later than originally scheduled.