He urged them not to disrupt the peaceful Friday prayers atmosphere with anti-government chants, witnesses said.
According to other witnesses, clashes occurred following the Friday prayers in the streets near the Tehran University.
A large number of protestors were shouting slogans against the government and chanted 'Death to Dictator' and (President Mahmoud) 'Ahmadinejad resign, resign'.
There was heavy traffic and most of the cars could not reach the prayer venue. Those stuck in traffic, however, showed victory signs and honked their horns.
Witnesses said that many protestors had come with the whole family, even their children. A lot of older people were also seen in the crowds.
On the Kargar Avenue, hundreds of protestors were carrying a huge green cloth in support of Moussavi. They also shouted 'Death to Russia' for Moscow's recognition of Ahmadinejad's re-election.
Except in front of the Tehran university and nearby streets, the police made no attempt to confront protesters, witnesses said.
Rafsanjani and Moussavi are fierce opponents of Ahmadinejad and have not acknowledged his re-election in June 12 voting, which was marred by accusations of fraud by the opposition.
Foreign reporters and photographers were prohibited by security officials from covering the Friday prayer ceremony or even staying outside the university to observe.