Conservative MP Fiona Bruce, who spearheaded the move, said the law was being "interpreted in different ways".
But her proposal was defeated by 292 to 201. A review of the extent of sex selective abortion was agreed to.
The government said it had been consistently clear that sex selective abortion was "already illegal".
Health Minister Jane Ellison new guidance had been issued by the Department for Health last May, which independent sectors had to comply with.
Ms Bruce had received support from more than 100 MPs prior to the debate.
Her amendment would not have changed the law, but sought to update 1967 legislation that was drafted before it was possible to identify the sex of a foetus.
An alternative amendment, providing for a review of the extent of gender selection abortion in England, Wales and Northern Ireland, was backed by 491 to 2.
Making the case for the change, the Congleton MP said her amendment would "clarify beyond doubt in statute that sex selective abortion is illegal in UK law".
And it would provide the government with an opportunity to address the "problem", such as by bringing forward best practice regulations and guidance, she added.
"Why is this new clause necessary? It is necessary because there is no explicit statement about gender selective abortion in UK law.
"The law is being interpreted in different ways because when the 1967 Abortion Act was passed, scans to determine the sex of the foetus were not available," she told MPs.
Ms Bruce insisted it would not criminalise any pregnant women because it applied only to doctors authorising an abortion.
And she rejected as "totally incorrect" the assertion that her proposal would block abortions based on a gender-linked disability.
Fellow Conservative David Burrowes lent his support to the amendment, telling MPs the law "does not expressly prohibit gender-selective abortions".
And the DUP's Jim Shannon, MP for Strangford, also endorsed the move, rejecting any assertions it would criminalise women. It would be doctors that were held to account, he said.
But Dr Sarah Wollaston, chairwoman of the Health Select Committee, was firmly opposed to the proposal, saying the amendment was "unnecessary" and could have "unintended consequences".
It could prevent women confiding in their doctor that they "feel under pressure" to abort their child because of its gender, as they may fear they will be criminalised, she told MPs.
Ms Wollaston said there was no evidence of a "systematic practice" of sex selective abortion in the UK, and warned against stigmatising communities by implying it was a widespread practice.
And the MP warned that the wording of the proposed clause would have implications for existing abortion laws, as it would "confer personhood on the foetus".
This point was echoed by Labour shadow health minister Luciana Berger, who said Ms Bruce's proposal would not address the causes of sex selective abortion.
She supported instead a separate amendment to require a review of the evidence of abortion on the grounds of sex in England, Wales and Northern Ireland.
For the government, Health Minister Jane Ellison said gender-based abortion was "abhorrent" but stressed that it was already illegal in the UK.
"The government has been consistently clear that abortion on the grounds of gender alone is already illegal.
"The Department of Health repeated this in guidance issued in May 2014 and it is important to stress that all independent sector providers have agreed to comply with and operate on the department's guidance and must do so as part of their licensing conditions," she said.
MPs have defeated a cross-party bid to clarify in law that abortion on the grounds of gender alone is illegal in the UK.