Cristina Fernandez de Kirchner was accused of shielding Iran from prosecution over the 1994 bomb attack against a Jewish centre in Buenos Aires.
Two out of three judges voted to reject an appeal by prosecutors, saying that no crime had been committed.
Cristina Fernandez de Kirchner has always denied the allegations.
The original decision to throw out the case against Cristina Fernandez de Kirchner was made by Federal Judge Daniel Rafecas in late February.
He made his conclusions after examining a 350-page report that had been prepared by special prosecutor Alberto Nisman before his unexplained death in January.
On March 26, the justice ministry said in a statement: “The federal appeals chamber ratifies the decision by Judge Daniel Rafecas to reject prosecutor Nisman’s accusation.”
The court of appeals agreed with Judge Daniel Rafecas’ conclusion that there was no evidence pointing to President Cristina Fernandez de Kirchner.
The sudden death of Alberto Nisman and the case against Cristina Fernandez de Kirchner has dominated Argentine headlines for much of this year.
The prosecutor was found dead in his apartment on January 18 with a bullet wound to the head and a pistol lying by his side.
Alberto Nisman had been only hours away from testifying in Congress against Cristina Fernandez de Kirchner and Foreign Minister Hector Timerman.
The circumstances of the prosecutor’s death are still unclear.
Earlier in March, Alberto Nisman’s family claimed independent tests showed that he was murdered.
The government has rejected any role in his death.
Cristina Fernandez de Kirchner said Alberto Nisman had been fed misleading information by a rogue intelligence agent who was trying to discredit her government.
Eighty-five people died in the car bomb attack on July 18, 1994 which completely destroyed the seven-storey Argentine Israelite Mutual Association (Amia) cultural centre in Buenos Aires.
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