Zimmerman, who has led Hebrew Union College-Jewish Institute of Religion since 1996, will undergo counseling and be prohibited from working as a rabbi until the Central Conference of American Rabbis reviews his case, at the earliest in two years.
A woman who answered the phone at Zimmerman's house in Cincinnati said Zimmerman, 58, "was not available."
The resignation, submitted Monday to the seminary's board of governors, caught the Jewish community by surprise, with associates reacting with "shock" and "sadness."
"Rabbi Zimmerman acted with great dignity in this case and accepted responsibility for his actions, and we're grateful to him for the manner in which he's responded," said Rabbi Eric Yoffie, president of the Union of American Hebrew Congregations, representing the country's 900 Reform synagogues.
Yoffie said the ethics committee of the Central Conference of American Rabbis--representing the country's 1,800 Reform rabbis--recommended Zimmerman be suspended, and the board upheld that recommendation on Monday. Burton Lehman, chairman of the school's board of governors, accepted Zimmerman's immediate resignation with "profound regret."
According to a statement released by the seminary, Zimmerman stepped down because of an "inquiry into personal relationships" before he became president in 1996.
Yoffie told The Dallas Morning News that Zimmerman did not contest the charges.
The seminary has appointed Provost Norman Cohen to serve as acting president, and a search committee will look for Zimmerman's replacement. "We are extremely proud of this institution, its faculty, its administrators and students, and look forward to their continued growth and success," Lehman said in a statement.
Yoffie said Zimmerman's resignation was greeted with "great shock and disbelief."
"He is a very much beloved figure in the movement and he's done wonderful work at Hebrew Union College, but in light of these events, there was no other course of action," he said.
An 11th-generation family rabbi, Zimmerman was born in Canada in 1942 and attended college at the University of Toronto. He was ordained at Hebrew Union College in 1970.
Prior to leading the seminary, he had served as senior rabbi at New York's Central Synagogue from 1972 to 1985, and senior rabbi of Temple Emanu-El in Dallas from 1985 to 1995. He also served as president of the Central Conference of American Rabbis from 1993 to 1995.
Rabbi A. James Rudin, the senior interreligious adviser for the American Jewish Committee and a columnist for Religion News Service, called Zimmerman a close friend and said Judaism has lost a great leader.
"The thing that is unique about him is that, yes, he was the head of the Reform seminary, but he brought with him a commitment to the whole Jewish community," Rudin said. "I am greatly saddened and disappointed. It's a great loss."
The seminary, with campuses in New York, Cincinnati, Jerusalem, and Los Angeles, is the main rabbinical training ground for Reform Judaism. It has ordained 2,328 rabbis, including 262 women. It ordained the country's first woman rabbi in 1972 and the first female cantor in 1975.