The state Court of the Judiciary, in a 50-page decision, cited Moore's "disregard for binding federal law" as a reason for the suspension.
Moore's term runs through January 2019. He is 69 and will be ineligible to run for re-election because of his age.
Friday's ruling also cited Moore's "history with this court," saying it was the second time he had been brought before the judiciary court for "actions grossly inconsistent with his duties as Chief Justice."
The chief justice made national headlines in 2003 when he defied a federal court order to remove a Ten Commandments monument from a public judicial building on the grounds that it was an unconstitutional endorsement of religion.
Both times, Moore's actions made him a hero to evangelicals, enraged liberals and caught the attention of the state judicial commission.
"The result in both instances has been a lengthy, costly proceeding for this court, the (Judicial Inquiry Commission), and, most unfortunately, the taxpayers of the State," the judiciary court ruling said.
Though Moore's defiance in 2003 cost him his job, he recaptured the top judicial post in a statewide election in 2012.
The Liberty Counsel — a nonprofit legal and education organization that promotes religious freedom — said in a statement that the suspension was "an unbelievable violation of the law" and "de facto removal from the bench."
"The rule of law should trump political agendas," said Mat Staver, Liberty Counsel chairman and one of Moore's attorneys.
"Sadly, today that is not the case," he said. "What this decision tells us today is that Montgomery has a long way to go to weed out abuse of political power and restore the rule of law."
Staver said Moore's administrative order directing probate judges to enforce the state ban on same-sex marriage "did not change the status quo."
"It did not create any new obligation or duty," he said in a statement. "To suspend Chief Justice Moore for the duration of his term is a miscarriage of justice and we will appeal this case to the Alabama Supreme Court. This case is far from over."
"Until further decision by the Alabama Supreme Court, the existing orders of the Alabama Supreme Court that Alabama probate judges have a ministerial duty not to issue any marriage license contrary to the Alabama Sanctity of Marriage Amendment or the Alabama Marriage Protection Act remain in full force and effect," Moore wrote at the time.
Moore has consistently fought against same-sex marriage.
In February 2015, he ordered lower court judges in Alabama not to implement a federal court ruling that overturned the state's ban on same-sex marriage. He later disputed a federal court order that directed all probate judges to cease enforcement of Alabama's marriage ban.
Americans United for Separation of Church and State, a religious liberty watchdog group, on Friday praised the judiciary court ruling.
"The people of Alabama are better off without Roy Moore on the court," the Rev. Barry W. Lynn, executive director of Americans United, said in a statement. "He is an embarrassment to the state, and his antics long ago became tiresome."
CNN's Ariane de Vogue and Kevin Conlon contributed to this report.