Modi, the first Indian Prime Minister to visit the Islamic Republic after 15 years on a bilateral visit after Atal Bihari Vajpayee, called on 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.
Khamenei, who has the final say over matters related to Iran's foreign policy and key issues, welcomed Modi.
Earlier in the day, Modi met Iranian President Hassan Rouhani and held one-on-one talks.
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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 USD 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.