A group of prosecutors organized the march in homage to Mr. Nisman, the special prosecutor investigating the 1994 bombing of a Jewish center here that left 85 people dead. Opposition political figures and Mr. Nisman’s former wife, Sandra Arroyo Salgado, a prominent judge, participated as rain fell.

The march, in a country sharply divided over his death, reflected the extent to which President Cristina Fernández de Kirchner has been put on the defensive since Mr. Nisman was found dead on Jan. 18 with a bullet wound to the head, after accusing her of trying to forge a secret deal to shield Iranians from responsibility for the 1994 attack.

Many people attending the so-called silent march were soaked by the time they reached the streets around the presidential palace on Wednesday evening. The demonstration was impressive in its reserved tone, with thousands just murmuring. If someone started yelling, someone else would yell, “Silence!”

Still, at one point, some in the march shouted in unison one word — justice — before going silent again.

Gonzalo Bordone, 25, a student, said he was fed up with what he viewed as government interference in the investigation into Mr. Nisman’s death. The demonstration was “a call for justice and, beyond that, an implicit show of general discontent with the government,” he said.

Investigators are seeking to determine whether Mr. Nisman was killed or committed suicide. His body was found just a day before he was scheduled to appear before Congress to discuss his criminal complaint against the president and several top supporters. He had also drafted a request for Mrs. Kirchner’s arrest, but did not include it in his complaint.

Mrs. Kirchner and Foreign Minister Héctor Timerman have rejected Mr. Nisman’s assertions, pointing to statements from Interpol’s former secretary general that they never sought to lift arrest warrants for Iranians. Still, a federal prosecutor revived Mr. Nisman’s case this month by seeking to charge Mrs. Kirchner in connection to the claims of secret negotiations with Iranians.

Before the march began, Mrs. Kirchner avoided speaking about it, but lashed out at what her government has described as meddling by the United States. Many are sensitive here to criticism by some American lawmakers of the Argentine government’s handling of the inquiry into Mr. Nisman’s death.

“We cannot allow them to transfer their conflicts here or try to provoke infighting between Argentines,” Mrs. Kirchner said.

In what appeared to be a swipe at the United States, she added that “in Argentina, the law rules,” while other countries “have clandestine prisons and people detained without trial.”

Meanwhile, senior officials in Mrs. Kirchner’s government bluntly criticized the demonstration. Defense Minister Agustín Rossi told reporters on Wednesday that the prosecutors who called for the march were “the battering ram of the political opposition.”

Still, political analysts said that the gathering reflected growing concern over judicial independence in Argentina, after Mrs. Kirchner publicly cast suspicion on a former spy chief and an aide to Mr. Nisman in the events surrounding his death. More broadly, tensions appear to be resurfacing over an attempt by Mrs. Kirchner to overhaul the judiciary in 2013.

“The government has done everything it can to anger the prosecutors,” said Martín Böhmer, a law professor at the University of Buenos Aires. “The split is political, and that’s what is behind this march,” he said, referring to continuing debates about how Argentina’s judiciary should operate after the return to democracy from military rule three decades ago.

In an open letter read aloud here on Tuesday night, pro-government writers claimed the prosecutors behind the march had been “sponsored” by news media organizations opposing Mrs. Kirchner, and described it as “undoubtedly sectarian and provocative.”

But for others, the demonstration was a sign of deeper problems in Argentina.

As the downpour soaked the crowd, many simply took slow strides beneath their umbrellas. The mood was generally reserved. Some held signs reading “Justice” or “Truth” or “Saving the judiciary is in our hands.”

“On one hand, there is the immediate plea to resolve the death of a prosecutor who had accused the president,” said Martín Lousteau, a former economy minister under Mrs. Kirchner who is now an opposition lawmaker.

“On the other hand, this is clearly a political march,” he added. “With Nisman, it’s like all the rot from bad political practices has surfaced in the sewers of the building where he died.”

Others marching in the rain agreed. “There is a sensation that the people are powerless in Argentina,” said Yael Pinco, 40, a computer technician in a gray raincoat. “The silent march is a way for us to come together to show the government that we are against their impunity.”

Some in the vicinity of the march, however, thought change could be achieved in other ways.

“There are other forms of protest and finding solutions, like voting,” said Sebastián Martínez, 35, a jewelry salesman. “You don’t see things like Nisman happening in other countries; they just don’t reach this point.”

Frederick Bernas and Charles Newbery contributed reporting.