Wiesenthal, who helped find one-time SS leader Adolf Eichmann and the policeman who arrested Anne Frank, died in his sleep at his home in Vienna, said Rabbi Marvin Hier, dean and founder of the Simon Wiesenthal Centre in Los Angeles.
"I think he'll be remembered as the conscience of the Holocaust. In a way he became the permanent representative of the victims of the Holocaust, determined to bring the perpetrators of the greatest crime to justice," Mr Hier said.
A survivor of five Nazi death camps, Wiesenthal changed his life's mission after the war, dedicating himself to tracking down Nazi war criminals and to being a voice for the six million Jews who died. He lost 89 relatives in the Holocaust.
Wiesenthal spent over 50 years hunting Nazi war criminals, speaking out against neo-Nazism and racism, and remembering the Jewish experience as a lesson for humanity. Through his work, he said, some 1,100 Nazi war criminals were brought to justice.
"When history looks back I want people to know the Nazis weren't able to kill millions of people and get away with it," he once said.
Calls of condolences poured into Wiesenthal's office in Vienna, where one of his assistants Trudi Mergili struggled to deal with her grief.
"It was expected," she said. "But it is still so hard."
The Israeli Foreign Ministry said Wiesenthal "brought justice to those who had escaped justice".
"He acted on behalf of six million people who could no longer defend themselves," ministry spokesman Mark Regev said yesterday. "The state of Israel, the Jewish people and all those who oppose racism recognised Simon Wiesenthal's unique contribution to making our planet a better place."
Wiesenthal was first sent to a concentration camp in 1941, outside Lviv, Ukraine. In October 1943, he escaped from the Ostbahn camp just before the Germans began killing the inmates. He was recaptured in June 1944 and sent back to Janwska, but escaped death as his SS guards retreated with their prisoners from the Soviet Red Army.
Wiesenthal's quest began after Americans liberated Mauthausen death camp in Austria where he was a prisoner in May 1945. He said he quickly realised "there is no freedom without justice," and decided to dedicate "a few years" to that mission.
"It became decades," he added.