Catholic gay rights groups say they are disappointed after bishops rejected proposals for wider acceptance of gay people, which had the Pope's backing.
The call to "accept and value" homosexuals was in a draft report, but failed to win the backing of two-thirds of the bishops at a synod in Rome.
The final report says only that anti-gay discrimination is "to be avoided".
Two other paragraphs suggesting divorced and remarried Catholics could receive communion also failed to pass.
The synod will meet again in a year's time for further discussion.
Excerpts from draft and final synod report
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.
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."
More than 200 bishops from around the world had spent two weeks at the Vatican discussing some of the most controversial issues around family life.
The gathering has revealed a fracture line in Church opinion over how to adapt traditional teaching on human sexuality to 21st Century attitudes, says the BBC's David Willey in Rome.
Pope Francis had made a powerful appeal to traditionalists not to lock themselves within the letter of the law, but conservative cardinals and bishops carried the day at the end of the synod, our correspondent adds.
On Sunday Pope Francis beatified one of his predecessors, Paul VI, who banned artificial contraception for Catholics in 1968.
The beatification is the final step before declaring someone a saint, and the move sends a strong message about the continuity of traditional Catholic teaching, our correspondent says.
The New Ways Ministry, a US Catholic gay rights group, said it was "very disappointing" that the synod's final report had not retained "the gracious welcome to lesbian and gay people that the draft of the report included".
But it added that the synod's "openness to discussion" provided "hope for further development down the road".
Another group, DignityUSA, said in a statement: "Unfortunately, today, doctrine won out over pastoral need.
"It is disappointing that those who recognised the need for a more inclusive Church were defeated."
However, Christopher Lamb, from British Catholic journal The Tablet, told the BBC the discussion at the synod had been a "huge achievement in itself".
It was important, he said, to remember that many of the bishops at the synod were from countries where homosexuality was illegal.
"We have now got an acceptance that we need a new language in the Church when talking about gay couples and homosexuality in general," he added.
Analysis: David Willey, BBC Vatican correspondent
Voting figures for the final document at the end of the synod show that Pope Francis received a rebuff in his attempt to persuade Church leaders to support his more merciful attitudes towards gay and divorced people. However, more than half still voted in favour of his proposed reforms.
Three crucial paragraphs in the final document all received more than 50% of the vote, although they failed to get the necessary two-thirds majority.
This allows the necessary leeway for further discussion before the synod reconvenes in Rome in an expanded form in a year's time.
Paragraph 55 of the final report, which has been rewritten many times during the past week, insists that although there can be no analogy between same-sex unions and marriage between a man and a woman, "men and women with homosexual tendencies must be welcomed with respect and delicacy".
Speaking after the vote, Pope Francis told attendees he would have been "worried and saddened" had there not been "animated discussions" or if "everyone had been in agreement or silent in a false and acquiescent peace".
In an address, he also cautioned against "hostile inflexibility... and not allowing oneself to be surprised by God".
The draft report said homosexuals had "gifts and qualities to offer to the Christian community".
Conservative groups described this as a "betrayal".
Cardinal Wilfrid Fox Napier of South Africa told Vatican radio on Friday "there were two issues that got people 'hot around the collar'".
"One was presenting homosexual unions as if they were a very positive thing," he said.
The second issue related to broken marriages "and the fact that people should be facilitated to get access to the sacraments", he added.