Cox Enterprises announced last night that it will close The Miami News after publishing today's editions despite a warning from the Justice Department that the company could face antitrust charges if it shuts the newspaper.

The final decision to close the 92-year-old News came after U.S. District Judge Stanley Marcus refused to grant requests by local groups to keep the newspaper open. A court order had been sought by a group trying to prevent Knight-Ridder Inc. from establishing a newspaper monopoly with The Miami Herald in the nation's 11th largest metropolitan area.Citing the guarantees of press freedom in the First Amendment, Marcus said that no U.S. judge has ever ordered a newspaper to print if it chose not to.

Atlanta-based Cox is closing the newspaper under an agreement with Knight-Ridder that will give Cox a share of the Herald's profits for the next 33 years. Cox could collect as much as $500 million under the agreement, said Steve Roof, attorney for the group trying to block the deal.

The two newspapers have shared advertising, printing and circulation departments under a federal law that grants exemptions from antitrust laws to promote competition in news reporting.

A year ago Cox and Knight-Ridder negotiated an amendment to their joint operating agreement that guarantees Cox a share of the Herald's profits even if the News goes out of business. Three months ago Cox put the News up for sale, saying the newspaper would be closed Dec. 31 unless a buyer was found.

The Justice Department's Antitrust Division two weeks ago launched an investigation of the deal. Attorneys said the antitrust exemptions granted by the Newspaper Preservation Act were not intended to permit a newspaper to pay its competitor to go out of business.

Yesterday, Justice Department Antitrust Chief Charles F. Rule urged Cox to continue efforts to sell the newspaper. Though Justice officials insisted that Rule's statement was "not a threat," Rule said the antitrust probe "will continue unless The Miami News is sold."

"We have concluded that the Miami joint operating agreement would likely lose its antitrust immunity once the amendment to it {closing the News} becomes effective," Rule said.Private antitrust lawyers say the government could try to stop Cox from collecting any of the Herald's profits under the agreement, or could attempt to force Cox to put up for sale its interest in the joint publishing venture with Knight-Ridder.

Cox has offered to sell only the name, the circulation list and the library of the News. The presses, typesetting systems and other equipment used jointly with the Herald are not part of the deal, making it impossible for any new owner to simply pick up where Cox left off.

"A conclusion that serious efforts by Cox would have resulted in the sale of The Miami News could provide the basis for an antitrust suit," Rule said.

One group of potential buyers had asked Cox to keep the newspaper open for a few more weeks so they could look for financing. Cox refused and executives yesterday said they don't know whether sale talks will continue."I think this is over," said publisher David Kraslow. "We're going down tomorrow."

The Miami News has been on the decline for years. The newspaper has run up losses of $90 million and its circulation has dwindled from 112,000 to less than 48,000, Cox said.

Cox owns the Atlanta Journal and Constitution and other publishing and broadcasting properties. Knight-Ridder's papers include the Philadelphia Inquirer and The Detrot Free Press.

Federal Courts have temporarily blocked Knight-Ridder's bid to form a joint operating agreement with The Detroit News, published by Gannett Co. Inc. of Rosslyn. Former Attorney General Edwin Meese approved the Detroit agreement over the objections of the antitrust division and his own advisers, only to have his decision overturned in court. A decision on the Detroit agreement is expected in early 1989.