France Football announced it would not present its annual award for the world's best player this year due to the coronavirus pandemic which halted some domestic competitions in 2019-20, including Ligue 1.
The decision has prompted suggestions Lewandowski has been harshly treated, having appeared the standout candidate to succeed Lionel Messi after his 55 goals fired Bayern to a stunning treble.
The striker, who was named Germany's Footballer of the Year, last week agreed he deserved the global honor.
Bayern chairman Karl-Heinz Rummenigge claimed earlier in August hope was not lost as FIFA had promised there would be a vote for the world's best player.
But Low, the Germany head coach, claims Bayern captain Neuer should pip Lewandowski to any award.
The goalkeeper was outstanding in the 1-0 Champions League triumph over Paris Saint-Germain, keeping Neymar and Kylian Mbappe at bay.
"Manu was in great shape throughout the 2019-20 season," Low told Kicker. "Manu is in a class of his own. Crazy, unbelievable.
"I have nothing against Robert Lewandowski - he is a top-class goalscorer - but, for me, the world's best footballer this year would be Manuel Neuer.
"What he has just done in this final round in Lisbon... He kept the door closed at the back.
"He had a very large role in winning the Champions League. Manuel was on hand in difficult situations against Lyon and Paris, otherwise it might be 0-1 or 1-1.
"You have the feeling that he is omnipresent."