The prosecutor who filed the case, Alberto Nisman, was found dead days after making the accusations. His death sparked outrage and conspiracy theories aplenty
Judge Daniel Rafecas on Thursday ruled that Nisman's case did not meet the minimum threshold to initiate a criminal investigation.
The government has denied the accusations from the beginning, and even some journalists who have pored through Nisman's report have said the case wasn't airtight.
The 63-page ruling states that "it is clear that neither of the two hypotheses of crimes made by the prosecutor in his complaint minimally hold up."
Nisman alleged that Argentina's government agreed not to go after Iranian suspects in the bombing in exchange for a favorable trade deal.
The two hypotheses that the judge referred to in his ruling were some of the key arguments made by Nisman.
The prosecutor argued that the Argentine government's decision in 2013 to form a joint "truth commission" with Iran to investigate the bombing would hinder an honest examination.
The 1994 bombing of a Jewish community center in the Argentine capital is the deadliest terror attack in the country's history. Eighty-five people were killed, and hundreds were injured.
Nisman also alleged that Fernandez and Foreign Minister Hector Timerman sought to withdraw from Interpol their requests for the arrests of several Iranian suspects.
The judge ruled that because the truth commission has never been created, it can't have functioned as an instrument to cover up anything.
Regarding Interpol, the judge said there is no evidence that the Argentine government took steps to have the international police body remove the so-called red notices against the Iranians.
Addressing the accusation against Fernandez, the judge wrote that "there is not one piece of evidence, not even a hint, that points to the current President regarding the instigating or planning of the grave crime of a cover-up. ..."
Nisman was found with a gunshot wound to his head in his apartment on January 18, a day before he was scheduled to testify before lawmakers about his accusations.
Authorities have yet to determine if his death was a suicide or a homicide.
Earlier this month, a new prosecutor who picked up Nisman's case said there was enough evidence to continue the criminal investigation.
Prosecutor Gerardo Pollicita filed a 61-page report essentially endorsing Nisman's allegations. Thursday's ruling quashed his request for the investigation to proceed.