The ad in Thursday's Journal is signed by hundreds of rabbis and was placed by Jewish Funds for Justice, a non-profit advocacy group, The Washington Post reported.
The group wants Ailes and Beck to stop talking about Nazis and the Holocaust and called on Fox News's owner, Rupert Murdoch, to impose sanctions on the pair.
Thursday is International Holocaust Remembrance Day, an observance established by the United Nations in 2005. Leaders of the Reform, Conservative and Reconstructionist movements, as well as Orthodox rabbis, signed the ad.
"We share a belief that the Holocaust, of course, can and should be discussed appropriately in the media. But that is not what we have seen at Fox News," the ad said.
This month, the group started a letter-writing campaign asking Murdoch to remove Beck from the air.
Beck's three-part program in November about liberal billionaire philanthropist George Soros prompted the ad, the report said.
The rabbis were offended when Beck described Soros as a "Jewish boy helping send the Jews to the death camps" during World War II.
Soros' Open Society Foundations has given the Jewish Funds group financial support.
The group was also angered over a November interview in which Ailes called National Public Radio officials "Nazis" for their decision to fire Juan Williams, who is also a Fox commentator.