He paid the £36.50 cost in full at Ashers' Belfast city centre branch but was telephoned two days later and told the company could not fulfil his order.
He said there was clear evidence Ashers believed it would have been "sinful" to have done so.
Through the legal proceedings, Daniel McArthur, the company's general manager, insisted Lee's sexuality was never an issue, rather the message he wanted the bakery to create.
Lee claimed the episode left him feeling like a lesser person.
In the original case, District Judge Isobel Brownlie ruled that religious beliefs could not dictate the law and ordered the firm to pay damages of £500.
Throughout the legal battle they have been supported by The Christian Institute, which has organised public rallies and garnered financial backing for the case.
Lee's case was taken in conjunction with the Northern Ireland Equality Commission.
The high-profile case was heard before three senior judges at Belfast's Court of Appeal in May where it was claimed the outcome would have implications for freedom of expression across the UK.
A lawyer representing the Northern Ireland Equality Commission submitted that the firm had not been forced to do anything against its beliefs.
Robin Allen QC told the court many businesses printed messages they did not associate with, and cited examples of posters made for election candidates.
Karen McArthur said as a born again Christian, she knew in her heart she could not make the cake but had taken the order to avoid a confrontation in the shop.
Daniel McArthur also told the court his family could not compromise their religious beliefs, despite the legal ramifications.
Ashers, a name with Biblical connotations, has six branches, employs over 80 people and delivers across the UK and Ireland.