Cristina Fernandez de Kirchner and Hector Timerman had been accused of covering up alleged Iranian involvement in a bomb attack against Amia Jewish centre in 1994.
Judge Daniel Rafecas said that there was no merit to the accusation as no crime had occurred.
The accusation came from prosecutor Alberto Nisman who was found dead last month in his flat.
Judge Daniel Rafecas said he would discontinue the case.
“The evidence gathered far from meets the minimal standard,” said a statement from Argentina’s judiciary system.
Alberto Nisman was due to testify in Congress against Cristina Fernandez de Kirchner when his body was found.
The circumstances of his death have not been clarified.
Cristina Fernandez de Kirchner said Alberto Nisman been fed misleading information by a rogue intelligence agent in order to discredit her government.
The president and the foreign minister had been accused of acting to hide their involvement in the Amia Jewish centre bombing – Argentina’s worst terrorist attack, in which 85 people died.
The lower house of the Argentine Congress has meanwhile approved a bill tabled by Cristina Fernandez de Kirchner scrapping the country’s secret agency, the Intelligence Secretariat.
The proposal was first announced days after Alberto Nisman’s death, on January 18.
A new federal investigative agency, which will be accountable to Congress, will replace it.
Cristina Fernandez de Kirchner said the change was overdue because the agency had remained largely untouched since the end of military rule in 1983.
The opposition accused the government of coming up with the proposal as a smoke screen for its involvement in the Amia bombing scandal.
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