"Our presence in Iraq and Syria is at the invitation of the governments of those countries to fight terrorism," Rouhani was quoted as saying in a telephone call with Macron.
Rouhani said "Iran does not seek to dominate" the region, but was instead working "for peace and security and to avoid the dismembering of countries".
The comments come days after France's foreign minister sparked Tehran's ire by accusing it of "hegemonic" ambitions in the Middle East.
Macron -- who has pledged to visit Iran in 2018 -- on Friday insisted that France wants a "dialogue" with Tehran.
Macron has been heavily involved in trying to defuse a crisis in Lebanon over the resignation of premier Saad Hariri that ramped up tensions between Iran and regional rival Saudi Arabia.