Without Friday's court action, the St. Louis clinic's license for providing abortions would have expired at midnight.
Judge Stelzer was careful to say his order took no sides in the ongoing dispute, but only found that a further hearing was warranted.
"A [temporary restraining order] does not purpose to pass upon the merits of a controversy or dispose of any issue," he wrote.
Planned Parenthood, however, met the standard that harm would result without a temporary restraining order, according to the court.
"Petitioner has demonstrated that immediate and irreparable injury will result if petitioner's license is allowed to expire," the judge wrote.
Abortion rights advocates outside the clinic cheered and exchanged high-fives when the ruling came down. They were cautiously optimistic in advance of Tuesday's hearing.
“I’m feeling pretty good," said Chris Kaufman, 61, in a pink Planned Parenthood shirt. "I’m still nervous but I’ll call it a win. We won the battle but there still a war."
Maud Essen, another advocate for abortion rights at the clinic, added: “The battle is not over, we will keep fighting, we’re grateful for this ruling and will keep fighting.”
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Anti-abortion protesters at the clinic said they were saddened by Friday’s ruling.
“I’m very disappointed, but we’ve had disappointments before and we will keep fighting and we will continue to be here to show these moms that they will be supported,” said Mary Maschmeier, 69, founder and president of Missouri-based Defenders of the Unborn.
The clinic appeared to be operating as normal throughout the morning and afternoon.
It is surrounded by a fenced parking lot and anti-abortion protesters on Friday approached cars waiting to get in. They handed the motorists leaflets with anti-abortion messages, though activists on both sides of the emotional debate said this is a common occurrence at the clinic.
Planned Parenthood officials hailed Friday's judicial reprieve, even if it is temporary.
“While we celebrate this temporary victory, we cannot forget that too many people are already forced to delay or entirely forgo care here in Missouri," said Dr. David Eisenberg, who is the medical director for reproductive health services of Planned Parenthood of the St. Louis Region.
“This is a great day for the people of Missouri but the fight is not over.”
The state of Missouri's health department has maintained that it has the right to ban abortions at the clinic if doctors who perform the procedure don't submit to questioning as a condition of license renewal.
Planned Parenthood says many of the doctors at the clinic are not their employees, so they can't force them to comply with the questioning.
Planned Parenthood claims the health department "is refusing to renew" its St. Louis clinic's license in a deliberate effort to shut it down.
Gov. Mike Parson said his administration will look forward to arguing in court that it's simply enforcing the state's standard regulations.
"Following today’s ruling, the state will soon have the opportunity for a prompt legal review of our state health regulators' serious health and safety concerns regarding Planned Parenthood’s abortion facility in St. Louis," he said in a statement.
"We are committed to and take seriously our duty to ensure that all health facilities in Missouri follow the law, abide by regulations, and protect the safety of patients."
Missouri is among half a dozen states that have recently passed sweeping new anti-abortion laws, sharply curbing women's access to the medical procedure.
Gov. Parson last week signed a bill that bans abortions on or beyond the eighth week of pregnancy, with no exceptions for rape or incest.
States with GOP-led legislatures are pushing anti-abortion measures in hopes of re-visiting Roe v. Wade, the landmark 1973 Supreme Court ruling that guaranteed women the right to terminate a pregnancy.
Conservatives hope the recent appointments of Justices Neil Gorsuch and Brett Kavanaugh have tilted the high court enough that it would reconsider Roe v. Wade.
In the highly contentious Kavanaugh confirmation last year, U.S. Sen. Susan Collins of Maine, a rare Republican who supports abortion rights, cast a key vote for the nominee. The centrist lawmaker said Kavanaugh told her Roe v. Wade was "settled law," making her comfortable with backing him.
Ali reported from St. Louis, Li reported from New York
Safia Samee Ali
Safia Samee Ali writes for NBC News, based in Chicago.
David K. Li
David K. Li is a breaking news reporter for NBC News.