Most of the case was thrown out last year. The judge conducted a hearing to decide if the last piece of the lawsuit should go as well.
The article was unusually tough and opinionated, even according to Time's own lawyer. It charged Scientology was a "ruthless global scam" posing as a religion. It said it was not a religion but an organization obsessed with making money.
Scientology was founded 41 years ago by science-fiction writer L. Ron Hubbard. It requires initiates to undergo teaching and counseling that can cost thousands of dollars.
The president of the church, the Rev. Hebber Jentzsch, said he was "astonished" by the ruling, but said he felt confident the church would prevail in the Court of Appeals.
"Here you have a multi-billion dollar colossus called Time- Warner and they use their billions of dollars to come after a small religious minority," Jentzsch said. "It was sort of like, well, I guess it's David and Goliath."
Time magazine issued a statement saying the suit should never have been brought in the first place.
"Scientology's efforts to punish Time for reporting about it have failed because of the First Amendment, and because of Time's willingness to defend its article and not be intimidated by the Church's apparently limitless legal resources."
In defending its right to publish its opinion, Time magazine reportedly wound up spending 7 million dollars in legal fees.
The Church of Scientology is no stranger to American courts. Its propensity to sue is well known and Time's attorney, Floyd Abrams fears that may intimidate some journalists.
"I know that there are some publications, including some very well-financed ones, that give Scientology a wide berth," Abrams said. "That's one of the effects of being viewed as a credible threat. And they are credible in terms of suing."
The federal court never heard testimony concerning the accuracy of the magazine article. The church first had to prove Time acted with actual malice. After ruling that the church had failed to do so, the judge dismissed the case.
Correspondent Christine Negroni and The Associated Press contributed to this report.