The ceremony held at Cologne's synagogue prompted an impassioned plea for the rite to be respected after a court in the western city controversially outlawed religious circumcision of boys in Germany.
"The hallmark of a free country is that it respects minorities and protects their rights," Ronald Lauder, president of the World Jewish Congress, told the ordination ceremony.
"Therefore I ask all the countries of your Europe: Choose freedom, choose tolerance, choose respect, and let us be Jews here," Lauder, who comes from the United States, added.
The court's judgement published in June that circumcision was tantamount to grievous bodily harm has united Jewish and Muslim groups in opposition and caused uproar from religious and political leaders in Israel and Muslim countries.
Diplomats admit the ruling has also proved "disastrous" for Germany's international image, particularly in light of its Nazi past.
Foreign Minister Guido Westerwelle, who attended the ceremony and has previously expressed concern over the debate, said Germany wanted a "flourishing" Jewish life but that meant being able to practice Jewish traditions without legal uncertainty.
"Religious freedom and religious traditions are protected in Germany and will continue to be protected. Whoever bars circumcisions of boys in Germany, bars Jewish life in Germany," he said.
The four rabbis, aged between 25 and 37 and hailing from Belarus, Israel, the US and Ukraine, were trained by the Berlin-based Hildesheimer's Rabbinical Seminary, which was founded in 1873 but forced to close in 1938.
It was reopened in 2009 as part of efforts to train German-speaking rabbis and contribute towards rejuvenating Jewish life in Germany.
The German parliament is expected to pass legislation on religious circumcision in the next few months.
About four million Muslims and more than 200,000 Jews live in Germany.