The vote by lawmakers "abandons the differentiated perception of various forms of partnership in order to stress the value of same-sex partnerships," said Archbishop Heiner Koch of Berlin, chairman of the bishops' Commission for Marriage and Family.
"But differentiation isn't discrimination, and same-sex cohabitation can be valued through other institutional arrangements without opening up the legal institute of marriage," he said.
Germany's parliament, or Bundestag, voted 393 to 226 with four abstentions to allow same-sex couples to marry.
Archbishop Koch said Article 6 of Germany's 1949 constitution stressed the heterosexual "classic marriage concept," adding that the Catholic Church would "face an increasing challenge" over the "vitality of Catholic marriage," but not change its "sacramental understanding" of marriage as a male-female union.
"As a church, we respect same-sex partnerships in which mutual responsibility and care are taken," he said.
"But it is worth noting how many who long fought the institution of marriage have now become fervent advocates of 'marriage for all,' and how prudent convictions about marriage have been abandoned citing changing times and popular moods," he said.
The vote was hurriedly arranged by Social Democrat Bundestag members for the last day of the legislative season. The action followed a June 26 magazine interview pledge by Chancellor Angela Merkel, a practicing Protestant who previously opposed same-sex marriage, to allow a free vote for her governing Christian Democratic Union.
However, while 70 Christian Democrats backed the measure, German media said prominent party members had vigorously opposed it, citing Christian convictions.
In a June 28 letter to parliament, Msgr. Karl Justen, director of the church's Catholic Office in Berlin, said constitutional protection for heterosexual marriage was confirmed by Germany's Federal Constitutional Court when it approved same-sex registered partnerships in 2002.
He said the Catholic Church recognized a "great diversity of family situations," but he insisted same-sex partnerships "cannot be equated with marriage."
Meanwhile, Thomas Sternberg, chairman of the lay Central Committee of German Catholics, which has previously backed liberal church reforms, told Passauer Neue Presse June 30 he also believed lawmakers had made a "serious mistake" by backing legislation that would require constitutional changes.
Same-sex marriage is legal in Norway, Sweden, Denmark , Finland, Iceland, Netherlands, Belgium, Spain, Portugal, Luxembourg, France, Great Britain (excluding Northern Ireland), and Ireland, and was backed by 83 percent of Germans in a 2017 survey by the government's anti-discrimination agency.
The measure was expected to be approved July 7 by the Bundesrat upper house for signing into law by President Frank-Walter Steinmeier.