PM Modi's visit comes months after lifting of international sanctions on Iran following Tehran's historic nuclear deal with the Western powers over its contentious atomic programme.
Prime Minister Narendra Modi today called on Iranian Supreme Leader Ali Khamenei, signifying the strength of the unique relationship between the two countries.
Mr Modi called on Mr Khamenei at his office towards the end of his two-day visit.
"A rare honour, signifying the strength of the unique relationship. Supreme Leader Ali Khamenei receives PM @narendramodi," External Affairs Ministry spokesman Vikas Swarup tweeted.
Mr Khamenei, who has the final say over matters related to Iran's foreign policy and key issues, welcomed PM Modi.
"Prime Minister of India H E Narendra Modi @narendramodi met with Leader of Revolution," said a tweet from his office.
Earlier in the day, PM Modi met Iranian President Hassan Rouhani and held one-on-one talks.
The two countries pledged to combat terrorism and radicalism as they signed 12 agreements including a "milestone" pact on developing the strategic Chabahar port, giving a boost to economic partnership in the post-sanctions era.
India also committed around $500 million for the important port in Iran's southern coast, which will serve as a "point of connectivity" between India, Afghanistan, Commonwealth of Independent States countries and East Europe.
PM Modi's visit comes months after lifting of international sanctions on Iran following Tehran's historic nuclear deal with the Western powers over its contentious atomic programme.