|President Fernandez's second term in office ends in December|
They had been accused of covering up alleged Iranian involvement in a bomb attack against a Jewish centre in 1994.
Judge Daniel Rafecas has concluded that there was not enough evidence to pursue the charges.
The accusation came from special prosecutor Alberto Nisman, who was found dead last month in his flat.
Judge Rafecas said he was throwing out the case after carefully examining Mr Nisman's 350-page report.
There was no proof that an agreement signed by the Argentine government with Iran in January 2013 was an attempt to shield the involvement of senior Iranian officials in the attack, the judge said.
'No legal basis'
The agreement was rejected by the Iranian government two months later and was never approved by Iran's parliament.
Defence Minister Agustin Rossi welcomed Judge Rafecas' ruling saying: "We have always said that Nisman's claims had no legal basis."
|Mr Nisman was found dead just hours |
before he was due to give evidence
to a congressional committee
But the BBC's Wyre Davies says the judicial system in Argentina is highly politicised and the decision to cease investigations will further polarise a dangerously divided nation.
Mr Nisman was due to testify in Congress against Ms Fernandez and Mr Timerman the day after his body was found.
The circumstances of his death have not been clarified.
President Fernandez said Mr Nisman been fed misleading information by a rogue intelligence agent. The government has rejected any role in his death.
|Thousands of people marched through the streets of Buenos Aires|
last week to demand justice for Mr Nisman
The proposal was first announced days after Ms Nisman's death, on 18 January.
A new federal investigative agency, which will be accountable to Congress, will replace it.
Ms Fernandez said the change was overdue because the agency had remained largely untouched since the end of military rule in 1983.
The opposition called the proposal a smokescreen for its involvement in the scandal.