Late last month, police conducting a routine security check found a brown paper bag containing the cash in Argentine pesos and US dollars in a bathroom cabinet inside Miceli's offices.
"The publicising of acts concerning my private life, relating them to my public activity, has caused undeserved damage to my honour which undoubtedly affects our government," Miceli said in her resignation letter.
The decision by Miceli, 54, came hours after a federal prosecutor requested she testify about the money.
Judicial authorities are probing where the money came from. Miceli has said her brother lent her most of the money for a planned property deal that was never carried out.
Miceli's resignation proved a political embarrassment for Kirchner three days before his wife, a prominent senator, is scheduled to launch her presidential campaign ahead of an October 28 vote.
In recent months, Kirchner has had to contend with a series of probes into allegations of corruption or irregularities by administration officials as his government prepares for the election.
A former president of the state-owned Banco de la Nacion, Miceli was named economy minister in November 2005.
Opposition politicians had harshly questioned Miceli's integrity after the money was found.
Miceli said she made a mistake by keeping the money in her office, but insisted she committed no crime.
Guillermo Marijuan, the prosecutor investigating the case, said Miceli should be questioned under oath to determine if she could be charged with malfeasance.
Marijuan traced the cash back to a bank he said the money came from, but failed to find any accounts there linked to Miceli or her brother.
He also found there was no record of a withdrawal for that amount of money at the bank.
"Such circumstances create ... sufficient suspicion that [the minister] covered up the spurious origin of the money found inside her office bathroom," the prosecutor said in a court statement.
Federal judge Daniel Rafecas, who is temporarily in charge of the investigation, will rule on whether Miceli should be called to testify in the case.
Tax evasion is rampant in Argentina, as is the perception that government officials pad their salaries with illegal gifts or bribes.