However, more than 70 members of Merkel's conservative bloc must have voted in favor of the bill for it to pass.
Merkel later explained her "no" vote by saying that she understood the definition of marriage in the German constitution as referring solely to unions between men and women.
She said, however, that she hoped the vote to approve gay marriage would lead to "more social peace.".
Fourteen European countries have now made gay marriage legal, with the Netherlands leading the way in 2001.
The long path toward same-sex marriage in Germany.
Germany currently allows civil partnerships, but not full marital rights, which would include the possibility to jointly adopt children.
Opinion: Angela Merkel's calculated change of heart on gay marriage. »