A document outlining the "gifts and qualities" homosexuals have to offer the Church failed to take the two-thirds majority it needed at the Family Synod in Rome.
Pope Francis was in favour of the original synod report, which said: "Homosexuals have gifts and qualities to offer to the Christian community...Are our communities capable of this, accepting and valuing their sexual orientation, without compromising Catholic doctrine on the family and matrimony?
"The Church affirms that unions between people of the same sex cannot be considered on the same level as marriage between man and woman."
Although more than 50% of the synod voted in favour of the draft it failed to attract enough support and was edited to say: "The Church teaches: 'No grounds whatsoever exist for assimilating or drawing analogies, however remote, between homosexual unions and God's design for matrimony and the family.'
"Nevertheless, men and women with homosexual tendencies should be accepted with respect and sensitivity. Any sign of unjust discrimination in their regard is to be avoided."
Other paragraphs suggesting divorced and remarried Catholics could take communion also failed to pass the meeting of more than 200 worldwide bishops.
American Catholic gay rights group New Ways Ministry said the decision in Rome was "disappointing".
But the group added that it took hope from the fact that more than 50% of bishops agreed with the document, which accepted the gifts and qualities of gay people.
"The synod's process and openness to discussion provides hope for further development down the road, particularly at next year's synod, where the make-up of the participants will be larger and more diverse, including many more pastorally-oriented bishops," it said in a statement.
Some bishops said the document did not conform to the teaching of Jesus Christ, and that the Church was trying to keep up with changing social attitudes.
The Voice of the Family group said the draft text was a "betrayal" and "one of the worst official documents drafted in Church history."
It added: "It is essential that the voices of those lay faithful who sincerely live out Catholic teaching are also taken into account. Catholic families are clinging to Christ's teaching on marriage and chastity by their fingertips."
Speaking after the synod, Pope Francis said there had been "a temptation to hostile inflexibility, that is, wanting to close oneself within the written word, and not allowing oneself to be surprised by God; by the God of surprises."
The pontiff added that he would have been "very worried and saddened" if all the bishops had agreed.
The synod will meet again in a year's time to discuss the issues again.