The closure of the papers, Shargh and Yas-e No, came on the eve of parliamentary elections that are expected to see conservatives wrest control of the Majlis from reformists, most of whom have been barred from standing.
They were the only two newspapers who dared to publish a letter from incumbent reformist deputies that questioned Ayat Allah Ali Khamenei's role in the mass disqualifications.
Some 70 reformists who resigned from parliament warned in the open letter of a "widening gap between the regime and the people" and asked if Khamenei had allowed the disqualifications of reformist candidates.
"The organs under your authority, having for four years humiliated the Majlis (parliament) and its deputies by blocking legislation, have openly blocked the most basic right of the people: to choose and be chosen," they said.
Criticising the supreme leader is a serious criminal offence in Iran.
The Tehran prosecutor's office closed the papers because they carried the stinging text despite an order from the Supreme Council for National Security - Iran's top national security body - not to do so, according to a leading press freedom activist.
"I condemn this decision. It is a way of restricting freedom of the press"
Association for the Freedom of the Press
"I condemn this decision. It is a way of restricting freedom of the press," Issa Saharkhiz of the Association for the Freedom of the Press said.
Officials went to the offices of the two newspapers to inform them of the ban. They also questioned two Shargh journalists, Saharkhiz said.
The official news agency IRNA quoted a Shargh employee as saying the paper had been shut "until further notice".
Iranians go the polls on Friday
"They told our editors that the final decision on Shargh will be announced officially on 21 February," the employee was quoted as saying.
A Yas-e No employee said the papers were padlocked by prosecutors later on Wednesday, and the sign on the building where the paper operates from was torn down.
Tehran's chief prosecutor, Said Mortazavi, several years ago ordered a major judicial crackdown on the press when he was head of Tehran's press court. On being promoted last year, he was quick to warn journalists to be even more careful.