The American Atheists lost their appeal on Monday, and the "Ground Zero cross" will remain at the 9/11 memorial site.
The atheists alleged that the cross violated religious freedom protections, but a three-judge panel found that the cross was not just a religious symbol.
The cross is a 17-foot tall, steel structure that was found in the rubble of the World Trade Centers after 9/11 by construction worker Frank Silecchia. First responders prayed and left messages and gifts at the cross, and the symbol later became a tourist attraction. The cross is currently part of the National September 11 Memorial & Museum.
The American Atheists first filed suit in 2011 against the Memorial & Museum and the Port Authority of New York & New Jersey, but the case was thrown out last year. Their appeal was dismissed Monday on the grounds that the cross is more a "genuine historical artifact" than a symbol of Christianity.
"The stated purpose of displaying The Cross at Ground Zero to tell the story of how some people used faith to cope with the tragedy is genuine and an objective observer would understand the purpose of the display to be secular," Judge Reena Raggi wrote on behalf of the panel.
"Taking hope from what he perceived to be a religious symbol, Silecchia brought the column and the cross-piece to the attention of other rescue workers, many of whom shared his reaction."
Shortly after its discovery, the cross was blessed by Franciscan priest Father Brian Jordan, who began conducting masses at the site.
"The Cross at Ground Zero thus came to be viewed not simply as a Christian symbol, but also as a symbol of hope and healing for all persons," Raggi continued.
The "stated purpose of displaying The Cross at Ground Zero to tell the story of how some people used faith to cope with the tragedy is genuine, and an objective observer would understand the purpose of the display to be secular."
Silecchia, who is now retired, thanked God for the court's decision.
"Faith won over atheism," he told the NY Daily News. "I'm kind of proud because that was my initial goal: to help ease the burden of humanity.
"All I can do is thank God for answering my prayer."
The American Atheists expressed disappointment in the ruling, and have not decided whether they will appeal the decision.