The tribunal rejected Gary McFarlane's claims, however, of religious discrimination and unfair dismissal.
Gary McFarlane was suspended by Relate Avon in March 2008 after he told his manager that his Christian beliefs meant he would not be able to offer sexual counselling for same-sex couples.
Relate said in a previous hearing that it had dismissed Mr McFarlane because he was not able to meet the requirements of its equal opportunities policy, which states that all clients must receive equal treatment regardless of their sexual orientation.
Andrea Minichiello Williams, Director of the Christian Legal Centre, said that laws preventing religious discrimination were "in danger of becoming a dead letter".
"The law is in a confused state; in the case of Lillian Ladele, the Islington Registrar, the Court held that Christian belief must give way to the rights of same sex couples; but in the case of Gary McFarlane there is a finding of wrongful dismissal," she said.
"The courts and public are confused; we call on the Government to recognise the legitimate expression of conscience by Christians in the area of sexual orientation and provide protection where necessary."
The ruling comes after an employment appeal tribunal ruled in December that a north London council had not acted unlawfully in disciplining a Christian registrar who refused to perform same-sex civil partnerships.
Mr McFarlane was represented by Paul Diamond, the same religious liberties specialist who represented check-in worker Nadia Eweida. She lost her religious discrimination case against British Airways last year after the airline banned her from wearing a Christian cross necklace.