The challenge, led by Lord Morrow of the Democratic Unionist Party, was defeated in the Lords last night, while up to 2,000 Christians demonstrated outside Parliament.
During the debate, Lord Rooker acknowledged that the Alliance had played a part in the Northern Ireland consultation.
The government has delayed its decision on similar regulations for England and Wales after it received more than 3,000 responses, mainly from faith groups.
Joel Edwards, General Director of the Evangelical Alliance, said: "We welcome the fact that the government recognised our constructive and full engagement in the process from the very beginning.
"The concerns about this legislation that we have been voicing all along have not gone away, and we will continue to hold the Government to account on its assurances that it will protect the rights of religious groups in practice.
"The strength of feeling among the Christian community on this issue, and the commitment to political engagement, was evident by the numbers and diversity of people who turned out at the demonstration.
"We support the principle of the law here - to defend people from discrimination.
"However, there is a danger that if a fair balance of rights is not achieved civil and religious liberties could be threatened."
In particular, Rev Edwards concluded, "Christians are not in favour of discriminating against gay people. But they don't want to find themselves coerced by law into facilitating the promotion of homosexuality.
"Freedom of conscience is an important right, which we intend to defend."