Less than two hours after the decision, Gov. Christie vowed to appeal, but he did not say whether he would seek a stay on the motion to prevent couples from starting to marry next month.
"Today means that finally couples in the state of New Jersey will have the dignity of marriage," said Troy Stevenson, executive director of Garden State Equality, who brought the suit. "It means they've been recognized and have the freedom of marriage."
Hayley Gorenberg, legal director of Lambda Legal, who tried the case, said, "We argued that limiting lesbians and gay men to civil union is unfair and unconstitutional, and now the court has agreed."
The motion was filed by six same-sex couples as part of the case Garden State Equality v. Paula Dow. The couples said civil union laws prevented them from receiving federal benefits they would be entitled to if same-sex marriages were permitted.
The state said the plaintiffs had the wrong defendant and should take up issues of inequality with the federal government and its agencies, as New Jersey treats civil unions and marriages equally.
But Jacobson said the state's civil union law was, by its very name, discriminatory.
"Whereas before . . . same-sex couples in New Jersey would have been denied federal benefits regardless of what their relationship was called, these couples are now denied benefits solely as a result of the label placed upon them by the state," she wrote.
Jacobson noted a trend among government agencies to limit benefits to married couples. Agencies cited in her decision include the Department of Labor, the Centers for Medicare and Medicaid Services, the IRS, and the State Department, which recognizes marriages only when determining spousal ability for immigration.
Other agencies have yet to redraft their policies after the June 16 U.S. Supreme Court decision.
With the decision in New Jersey, Pennsylvania becomes the only state in the Northeast where same-sex marriage is illegal.
Christie's press secretary issued a statement reiterating his push to put the question on the November ballot and his intent to appeal the judge's ruling.
"Since the Legislature refused to allow the people to decide expeditiously, we will let the Supreme Court make this constitutional determination," the statement said.
Christie's Democratic opponent in November, State Sen. Barbara Buono, called the ruling "a stark reminder that Gov. Christie stands on the wrong side of history. At every turn, he has prevented our gay brothers and sisters from enjoying the same rights as other New Jerseyans."
"The courts have spoken and the people have spoken. It is time for Chris Christie to stop blocking equal rights for all New Jerseyans," she said in a statement.
An appeal and subsequent decision could take months. To stay the order, the state must prove marrying couples while the case is under appeal would cause "irreparable harm" to the state.
"It's going to be hard proving irreparable harm is being done by allowing loving committed couples to get married, but there's still that opportunity," Stevenson of Garden State Equality said.
Meanwhile, legislators continue to attempt to override Christie's veto of a bill that would legalize same-sex marriage.
Politicians and interest groups were quick to weigh in on Friday's ruling.
"I am thrilled this court decision now brings us closer to fulfilling our nation's promise of equality," U.S. Sen. Robert Menendez (D., N.J.) said in a statement.
Udi Ofer, executive director of the New Jersey chapter of the American Civil Liberties Union, said the court "recognized the love and commitment that same-sex couples share is no different from anyone else's."
Len Deo, president of the New Jersey Family Policy Council, denounced the decision.
"What disturbs me more than anything else is instead of letting the people weigh in on this . . . that judicial activism rules again," Deo said.
He said he was concerned whether religious organizations could receive exemptions if they did not want to perform same-sex marriages.
Two legal experts predicted the ruling would stand.
Frank Askin, director of the Constitutional Rights Clinic at Rutgers School of Law in Newark, said that the decision was inevitable after the repeal of the Defense of Marriage Act, and that he thought Christie was wasting his time by appealing.
Ronald Chen, acting dean at Rutgers-Newark Law, wrote amicus briefs for the case and called the logic of the ruling unassailable.
"Unless the New Jersey Supreme Court overrules its prior precedents, it should affirm this ruling," he said.
If the order is not stayed, Chen said, any marriage license issued as of Oct. 21 would remain valid, regardless of the court's ultimate decision.
"Once they're married, they're married," he said.
Inquirer staff writer Maddie Hanna contributed to this article.