Early projections gave the AfD 13.5 percent of the vote, allowing it to enter the Bundestag for the first time, as Germany's third-biggest party.
The far-right has not been represented there since the 1950s—a reflection of Germany's efforts to distance itself from the horrors of the Nazi Holocaust.
"We trust that centrist parties in the Bundestag will ensure that the AfD has no representation in the coming governing coalition," the EJC said.
"Some of the positions it has espoused during the election campaign display alarming levels of intolerance not seen in Germany for many decades and which are, of course, of great concerns to German and European Jews."
Last year, a regional lawmaker for the anti-immigrant AfD quit the party after a row over his allegedly anti-Semitic views had threatened to cause a damaging split in the party.
Wolfgang Gedeon, a former doctor turned AfD lawmaker, triggered outrage by saying that denial of the Nazi Holocaust, in which six million Jews were murdered, was a legitimate expression of opinion, describing Holocaust deniers in the past as "dissidents."
He also drew criticism for saying that "Talmud Judaism is the inner enemy of the Christian West." Holocaust denial is a crime in Germany.
Leading up to the elections, Salomea Genin, an 85-year-old Jewish Berliner who fled the Nazis as a child, said she would flee Germany a second time if the AfD ever took power.
Genin, who holds dual German and Australian nationality, was shocked by comments this month by a top AfD candidate in Sunday’s federal election, Alexander Gauland, that Germans should take pride in what their soldiers achieved in two world wars.
“I was speechless,” said Genin, who lost 29 family members during the Holocaust, in which the Nazis killed six million Jews. “I never thought that I would again face a movement in Germany with the sort of ideas that are coming out of the AfD.”