John Mason had hoped to alter the legislation to ensure no one is "compelled by any means" to solemnise gay marriage.
After his attempts to add "protection" for religious groups were rejected, Mr Mason said he hoped individuals, couples or organisations would not be penalised for supporting a traditional view of marriage, though he said he remained sceptical.
But the Shettleston MSP added: "The debate within the SNP has been good and I got on particularly well with Marco Biagi."
Just as Mr Mason was a quiet stalwart of the opposition case on Tuesday, so Mr Biagi spoke in favour of the reform.
The SNP did face one rebellion when South Lanarkshire Councillor and Minister Bev Auld resigned from the party over the vote in favour of same-sex marriage, but it was claimed that this was a one-off which had been long threatened.
The campaign in favour of equal marriage woke up with a celebratory hangover after a party in a bar near the Scottish Parliament.
Tom French, of the Equality Network, said Scotland now has one of the most progressive equal marriage bills in the world.
He said: "That's why the Equality Network strongly believes the time spent considering and consulting on the bill has been well-and-truly worth it."
But Rev David Robertson, Free Church of Scotland minister in Dundee and director of the Solas Centre for Public Christianity said: "It was with a heavy heart that we listened to the debate in the Scottish Parliament."