Peter Kemmether, a 62-year-old father of four children, took part in the ceremony led by Bishop Gerhard Ludwig Müller on Tuesday evening in the Bavarian city.
He had been a protestant pastor, but converted to Catholicism.
In similar cases the Vatican has been known to make exceptions to its insistence on clerical celibacy, and the Congregation for the Clergy there approved the decision after Kemmether completed various courses in Catholic theology, the diocese said.
According to the German Conference of Bishops, Protestant pastors have become Catholic priests on several occasions in the past, but a spokesperson said the organisation could not provide specific numbers.
The Church in Bavaria in particular has ordained several former Protestants into the priesthood in the last decade.
These men have papal permission to carry on with their family lives as usual, and are not required become celibate.