The Mannschaft team manager was baffled as to why supporters felt compelled to jeer the Arsenal playmaker when he was withdraw late in the game in Stuttgart
The Arsenal playmaker was named his country's Footballer of the Year in January and received his award on the pitch before kick-off before then setting up the only goal of the game.
However, Ozil was roundly jeered when he was substituted in the 89th minute, much to the bemusement of Bierhoff.
"At the time, with the score [at 1-0], I did not understand the whistles. I find it a pity that a player like Mesut is singled out," the Germany team manager told der Westen.
Joachim Low's men were often on the back foot against Chile, who pressed high up the pitch and carved out a number of openings, and the fans at the Mercedes Benz Arena also made their frustrations known by booing the whole team at the final whistle.
Low admitted that the South Americans were "clearly better" than Germany in the second half, while Philipp Lahm admitted his side were "lucky" to record victory and that the supporters are entitled to feel aggrieved at their performance.
"The fans paid to see this match and they wanted a better performance, you have to accept [the jeers]," the Bayern Munich defender told ARD. "We have some work ahead of us and we are aware of that."