Some 60 hardline Islamists chanted "Death to America" and "Death to Israel" as Rouhani's motorcade drew out of Tehran's Mehrabad Airport.
But they were outnumbered by 200 to 300 supporters of the president who shouted: "Thank you Rouhani."
A small police contingent separated the rival demonstrators.
The shoe missed the car and Rouhani stood up through the sunroof to acknowledge the crowds.
Before leaving New York where he attended the UN General Assembly, Rouhani had a 15-minute telephone conversation with Obama on Friday, the first contact between leaders of the two countries in more than three decades.
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