The 40-year-old was jeered by home supporters every time he touched the ball as Bayern Munich were held to a goalless draw at the Veltins-Arena, ending the champions' run of 67 consecutive matchdays top of the Bundesliga table and denying newly promoted Schalke's first win over their old rivals since 2011.
Neuer left Schalke for Bayern in the summer of 2011 and has been the Bavarian club's undisputed first choice ever since, extending his contract in May to keep him at the Allianz Arena until the summer of 2027.
He has previously indicated this is likely to be his final season as a professional, meaning Saturday's trip to Gelsenkirchen, his home town, may have been his last competitive appearance there.
Schalke, back in the top flight after three years in the second division, picked up their first point of the season under coach Miron Muslic, with goalkeeper Loris Karius denying Bayern a late winner with a fine save from a long-range effort.
"Manuel has repeatedly emphasised that he has a Schalke heart. That's why I think it's a real shame," Schalke sporting director Frank Baumann told Bild. "I would have wished for something else."
Some of the reception went beyond ordinary rivalry, with Bayern sporting director Max Eberl separately criticising a section of the home crowd for using personal insults rather than simply booing. Baumann suggested a future role at the club could not be ruled out if Neuer wanted to return home after retiring.
"There hasn't been any discussion in that direction yet, but I definitely wouldn't rule it out," he said. "Fundamentally, I think it's interesting to involve former players because of their qualifications and passion."
Neuer himself brushed off the reception after the match.
"Those are actually compliments, that's love. Every boo every time I touched the ball was a compliment," he said. "I played here for over 20 years, so it was still a very emotional day for me — something truly special. Still, I would have liked to take the three points home with me."