A government spokesman said Mr Larijani had resigned several times but President Mahmoud Ahmadinejad has finally accepted his resignation.
Saeed Jalili, Iran's deputy foreign minister for European and American affairs, has been named as the new chief nuclear negotiator and Iran's meeting with EU foreign policy chief Javier Solana is to go ahead as planned.
A government spokesman said there would be no change in Iran's atomic programme.
Mr Larijani said earlier this week that he would hold fresh talks with Mr Solana next Tuesday in Rome on Iran's nuclear stand-off with the West.
Despite several meetings during the past year, the two have not overcome the deadlock over Tehran's refusal to suspend its sensitive uranium enrichment activities.
Mr Solana must report to major world powers Britain, France, Germany, Russia, China and the US before mid-November on Iran's willingness to give up uranium enrichment in exchange for political and trade incentives.
The West believes Iran's nuclear programme is cover for a drive to develop an atomic bomb, but Tehran insists it is for civilian objectives only.
