The former premier said he was "a historic friend of the Jewish people and the state of Israel" and it was "surreal to attribute to me anti-German sentiment or a presumed hostility towards the German people, to whom I am a friend."
The 77-year-old's statement, posted on the website of his centre-right Forza Italy party, came after an international outcry over his claim on Saturday that Germans denied the existence of Nazi concentration camps.
The media mogul, who is campaigning for the European elections on behalf of his party despite a tax-fraud conviction, made the comment while lashing out at European Parliament chief Martin Schultz, the centre-left candidate in the race to lead the EU Commission.
The affront came as he was defending comments made in 2003, when he offered Schulz a part in a film as a "kapo", a camp inmate overseeing prisoners.
His comments sparked fresh outrage, with Jean-Claude Juncker - Schultz's main opponent and a member of the same umbrella centre-right European People's Party as Berlusconi - saying the statements "sickened me".
"I call on Mr. Berlusconi to withdraw his statements immediately and to apologise to the survivors of the Holocaust and to the citizens of Germany," he said in a statement on Monday.
The German government dismissed the remarks outright as "absurd", declining to comment on them.