Missionary siblings Rembertus Cornelis Beerepoot and Fanny Alida Beerepoot, of Tasmania, stopped paying the tax from 2011. This lead to their farm being seized and sold by their local council in 2017.
Solicitor Stephen Linden told the court the pair had been served two notices of their debt and had failed to supply their tax returns.
Mr Beerepoot argued that God's law is the "supreme law of this land".
He told the court: "We believe that the constitution affirms the fact that the Commonwealth resides within the jurisdiction of the law of the Almighty God and the law of the Almighty God is the supreme law of this land.
"Transferring our allegiance from God to the Commonwealth would mean rebelling against God and therefore breaking the first commandment.
"As we reject God, the curses upon us become greater, but if we return to God's teachings there will be healing.
"We rely on the blessings we receive from God which we give to him and not to an outside entity such as the tax office."
However, in his judgement, Associate Justice Stephen Holt questioned the biblical link to abstaining from paying taxes.
Justice Holt explained: "I believe the submissions to be honestly and genuinely held beliefs rather than an attempt to avoid tax liabilities.
"But in my view, the Bible effectively said that civil matters and the law of God operate in two different spheres."
Justice Holt ordered Ms Beerepoot to pay A$1.17m and Mr Beereport A$1.16m - to cover "income tax, administrative penalties and general interest charges" and other costs, court documents show.
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.
