On the sixth day of protests that have cost 21 lives, according to official figures, Macron told Rouhani that he was worried about the number of victims and insisted that "fundamental liberties, especially freedom of expression and demonstration, must be respected".
He called on Rouhani to exercise "restraint and appeasement".
The pair agreed to postpone a visit scheduled for this week by French Foreign Affairs Minister Jean-Yves Le Drian without naming a new date.
Le Drian's trip was to prepare the way for a visit by Macron later in the year.
Iran calls for action against exiled group
Iranian state television reported that Rouhani called on Macron to take action against the Mojahedin-e-Khalq (MEK), an exiled opposition group that is currently based in Auvers-sur-Oise, north of Paris.
The Iranian government describes the organisation as a "terrorist group" and it was on the European Union's terrorist list until 2009.
Tehran claims that it has stirred up the current demonstrations on the orders of Saudi Arabia and "certain European countries".
"We criticise the fact that a terrorist group has a base in France and acts against the Iranian people and encourages violence," Rouhani said, according to the TV channel.
The accusation was a reflection of the "panic of the mullahs' regime in the face of the extent of the uprising against the religious dictatorship", MEK national council member Afchine Alavi said in a statement.
Rouhani and Macron also discussed the situation in Iraq and Syria, with the French president calling for "strengthened dialogue on arms control, including ballistics, in the region".