The case, in Pennsylvania, has been closely watched as the key legal battle in an ideological war waged by Christian activists to debunk Charles Darwin's theory and to challenge the principles of secular education.
Advocates had hoped to introduce intelligent design into schools across the United States - despite claims by critics that it violates the separation of church and state.
The concept holds that nature and biological structures are so complex that they must have been designed by an unidentified intelligent being rather than evolving by chance.
"Our conclusion today is that it is unconstitutional to teach ID as an alternative to evolution in a public school science classroom," US District Court Judge John Jones ruled.
The school board in the northeastern state's Dover area had ruled that biology classes must include teaching of the intelligent design concept.
But Jones concluded in his 139-page ruling that intelligent design violated the "establishment clause" of the First Amendment to the Constitution, which bars a state-mandated religion.
"In making this determination, we have addressed the seminal question of whether ID is science. We have concluded that it is not," he wrote.
Jones reasoned after hearing six weeks of testimony that "ID cannot uncouple itself from its creationist, and thus religious, antecedents".
"Intelligent design is not science. Intelligent design is about religion"
The judge also lashed out at activist members of the Dover school board, eight of whom were voted out of office in November, for thrusting an "untestable alternative hypothesis" to evolution into the classroom.
"The citizens of the Dover area were poorly served by the members of the board who voted for the ID policy," he said, accusing the board of "breathtaking inanity".
"It is ironic that several of these individuals, who so staunchly and proudly touted their religious convictions in public, would time and again lie to cover their tracks and disguise the real purpose behind the ID policy."
Opponents of intelligent design described the ruling as "wonderful".
"This is a very important decision, judge Jones has reaffirmed that in this country, public servants shall not use their public office to impose their religious views on others," said Stephen Harvey of law firm Pepper Hamilton, which fought the case.
Plantiff Tammy Kitzmiller, a parent who brought the case, said "intelligent design is not science. Intelligent design is about religion".
But supporters of the theory said they had simply lost a single battle.
"Anyone who thinks a court ruling is going to kill off interest in intelligent design is living in another world," said John West, of the Discovery Institute think tank, which advocates intelligent design.
The ruling was the latest in a flurry of court judgments on the role of religion in US society, which has also seen Supreme Court justices rule on the proper use of the Ten Commandments on state property.
"Anyone who thinks a court ruling is going to kill off interest in intelligent design is living in another world"
Discovery Institute think tank
The intelligent design trial has drawn comparisons to the Scopes trial of 1925, in which a biology teacher was convicted of violating Tennessee law by teaching evolution - in a precedent-setting case on the role of the Bible in US public life.
Of Pandas and People
In an October 2004 vote, the Dover School Board required teachers to read pupils a statement stating that Darwin's "theory of evolution" was not a "fact" and contained "gaps".
Students were also to be informed about an intelligent design textbook called Of Pandas and People.
Jones said the statement misrepresented Darwin's theory without offering scientific justification and offered students an alternative based on religion and not science.
And he accurately predicted the reaction of intelligent design advocates, in this politically sensitive case.
"Those who disagree with our holding will likely mark it as the product of an activist judge. If so, they will have erred."
Discovery's West hit back: "This is an activist judge who has delusions of grandeur."