The announcement comes three weeks before Iran and the UN atomic watchdog are to resume talks in Vienna over Tehran's controversial nuclear programme.
Until now, Tehran's point man has been Saeed Jalili, head of the Supreme National Security Council. That follows a tradition dating back to 2003, when Rowhani himself headed the council.
In recent weeks, the press had speculated that Zarif, who worked with Rowhani when he held the job until 2005, would be taking over the talks.
Western countries and Israel suspect Iran's nuclear programme is cover for a drive for a weapons capability, an ambition Tehran strongly denies.
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The IAEA has been probing the programme for a decade, and a number of international sanctions have been slapped on Tehran for its refusal to stop enriching uranium. That process can lead to producing the fissile core of an atomic weapon.
Talks between Tehran and major world powers have so far failed to yield an agreement.
Delegates from the IAEA and Iranian officials have held 10 rounds of failed meetings since the November 2011 publication of a major IAEA report on Tehran's nuclear programme.
Director-general Yukiya Amano expressed his frustration in June at talks that were "going around in circles".
The IAEA wants Iran to grant access to sites, documents and scientists involved in Tehran's alleged efforts to develop atomic weapons, which the agency suspects mostly took place before 2003 but are possibly still ongoing.
In its quarterly report, seen by AFP last week, the IAEA said Iran had installed hundreds more centrifuges since May that could enable it to enrich uranium faster. That would allow it to obtain the amount of fissile material needed for a nuclear bomb more quickly, if it wished to go down that path.