A government official said on Monday that Ayatollah Ali Khamenei opposed the move by Mahmoud Ahmadinejad to allow women on to the stands - a suggestion which caused a furore in the clerical establishment.
"Iran's Supreme Leader has instructed the government to consider the religious leaders' views and reverse its decision," government spokesman Gholamhossein Elham said.
"The government will act based on this instruction," he said.
It marked the first time Khamenei, who has the final word on matters of state in Iran's system of clerical rule, has openly challenged government policy since Ahmadinejad's inauguration last August.
Several high-ranking clerics had criticised Ahmadinejad's announcement last month that women would be permitted to watch men compete in sports stadiums for the first time since the 1979 Islamic Revolution.