Iranian newspapers hailed the first contact with a US president in more than three decades as the ending of a long taboo.
But his 15-minute conversation with the leader of a country long derided as the "Great Satan" was too much for some hardliners.
Nearly 60 gathered outside Tehran's Mehrabad Airport, chanting "Death to America" and "Death to Israel" as his motorcade passed.
They were outnumbered by 200 to 300 supporters of the president chanting: "Thank you Rouhani," who were separated from the protesters by a small contingent of police.
The shoe was thrown as Rouhani stood up through the sunroof of his car to acknowledge the crowd. It failed to hit its target.
There have been no diplomatic relations between Tehran and Washington since radical students took hostages at the US embassy in the aftermath of the 1979 revolution.
Dubbed the "nest of spies" by the regime, the old embassy site has since been the scene of annual commemorations which have been the focal point for hardline anti-US sentiment.
The airport protest contrasted with the plaudits Rouhani received from the Iranian press for the historic telephone call.
Rouhani told reporters at the airport that it had been Obama's initiative to make the call.
"We were going to the airport, when I was informed that the White House had called the cellphone of our ambassador to the UN," his office quoted him as saying.
"I was informed President Obama wanted to speak to me for a few minutes."
Iranian newspapers crowed that Rouhani had wrong-footed the world's media by taking the US president's call after coverage of his keenly-awaited visit to the United Nations in New York had focused on the lack of a face-to-face meeting.
"The world caught unawares," crowed reformist daily Arman. "International media in shock over the telephone call."
The Etemad newspaper carried a photomontage of Rouhani and Obama side by side. "Historic contact on way home," read a banner headline taking up the whole front page.
'Both sides must be careful'
But the paper carried an opinion piece by international relations professor Mohammad Ali Bassiri warning of the challenges that lie ahead to bring about a full rapprochement, not least the opposition of US ally and
"These contacts and meetings between Iran and the United States have extremist opponents and both sides must be very careful," Bassiri wrote.
"Many countries, notably the Zionist regime, believe their interests will be jeopardised by a normalisation of relations between Iran and the United States and will seek to stop it."
Israeli Prime Minister Benjamin Netanyahu, who has described Rouhani as a "wolf in sheep's clothing," is to meet Obama on Monday before addressing the UN General Assembly on Tuesday.
Former president Akbar Hashemi Rafsanjani, widely seen as Rouhani's mentor, said the incumbent had pulled off a diplomatic coup by speaking to, but not meeting, Obama.
"The fact that Obama asked our president to meet him but the latter said it's too early and we must prepare the ground is the very triumph that God promised us," Rafsanjani said in comments widely reported in the Iranian press.
The commander of the covert operations unit of the elite Revolutionary Guards said the attention lavished on Rouhani in New York was a vindication of Iran's tough defence policy.
"The respect shown by the world to President Rouhani is the fruit of the nation's resistance," General Ghassem Soleimani was quoted as saying.
The Qods Force, which Soleimani commands, lies at the centre of US allegations of Iranian state sponsorship of terrorism, one of a raft of issues, over and above Iran's controversial nuclear programme, that Rouhani is going to have to tackle in any rapprochement.
Many newspapers carried front-page photographs of a smiling Foreign Minister Mohammad Javad Zarif and Secretary of State John Kerry at nuclear talks in New York between Iran and the major powers.
Zarif said he hoped for a deal within a year to allay international concerns about Iran's nuclear ambitions.
But Zarif's Western counterparts made clear at the meeting that an agreement will require big concessions from Iran.
They include the suspension of all enrichment of uranium beyond the level required to fuel nuclear power plants, and the closure of Iran's underground enrichment facility near the central city of Qom.
Back home after the international fanfare, Rouhani now has to persuade sceptics within the regime that they are concessions worth making.
