The two and a half tonne sculpture was housed at the state court building until Wednesday, but no more.
Workers pulled the granite monument, seperated into two, out of view to another location in the building for storage.
"We have lost the battle but not the war," said a determined Reverend Rob Schenck, one of the organisers and president of the Washington-based National Clergy Council.
Last week, Alabama Supreme Court Justice Roy Moore said he had no intention of removing the Ten Commandments from the public building.
But a federal court ruling by US District Judge Myron Thompson said it violated a constitutional prohibition on government promotion of religion.
The federal court had ordered the removal of the display placed in the state justice building in Montgomery by 20 August. But Moore vowed to ignore this and asked the US Supreme Court to squash Thompson's order.
Schenck promised the next strategy would be to approach lawmakers state-by-state to come up with legislation to permit Ten Commandment displays in public places. The idea is called "the Ten Commandments Dissent Act," he explained.
Nevertheless, eight associate justices ordered the building manager to remove the statue of the Judeo-Christian commandments while future litigation is discussed.
The controversial carving was
seperated into two pieces
The monument might also be able to be put back on display if legally it were declared a historic monument, thus distinguishing it from the strictly religious one.
In this instance, the First Amendment of the US Constitution establishing the separation of church and state would not come into play.
Schenck called the statue's removal a morally cowardly act and told CNN he was disappointed with the building's management and the eight other justices on the court.
But "I think this will only strengthen our resolve," he told the cable network.
Another leader of the demonstrators, Reverend Patrick Mahoney, observed: "If this monument is so horrible ... so unconstitutional, why leave it in the building?"
Mahoney also promised “the final chapter has not been written
on this, and we’re still moving forward”.