A government spokesman said Mr Larijani had repeatedly offered his resignation and President Mahmoud Ahmadinejad had finally accepted it.
Mr Larijani had differences with the president over how to proceed with the negotiations, correspondents say.
Western countries suspect
The spokesman, Gholam Hossein Elham, said a deputy foreign minister, Saeed Jalili, would replace Mr Larijani in time for a meeting on Tuesday with the European Union's foreign policy head Javier Solana.
Russian proposals?
The BBC's Jon Leyne, in
Mr Larijani has favored further negotiations with the West over
The resignation comes just days after Russian President Vladimir Putin visited
Some Iranian media reported that Mr Putin had offered new compromise proposals over the stand-off with some Western countries.
Media close to President Ahmadinejad, however, have denied that the Russian president made new proposals.
The resignation is a sign, says BBC correspondent, that
Although Mr Larijani is a conservative who was appointed by Mr Ahmadinejad to be
The UN Security Council is waiting for reports from the EU's Mr Solana and from the UN's nuclear watchdog, the IAEA, before deciding on a third round of tougher sanctions against
Some Western countries, led by the
The IAEA says there are outstanding questions about
PHOTO CAPTION
Ali Larijani