Iran's leaders have claimed that the weeklong meeting, which wraps up Friday, displayed the futility of Western attempts to isolate the country over its nuclear program.
But Iran also was forced to endure criticism from Morsi and another high-profile guest, U.N. Secretary-General Ban Ki-moon, who cited concerns about Iran's human rights record and called its condemnations of Israel unacceptable.
It's highly unlikely that Iran would abandon Assad as long as there is a chance for him or at least the core of his regime to hang on. Iran counts on Syria as a strategic outlet to the Mediterranean and a conduit to its anti-Israeli proxy Hezbollah in Lebanon.
But the meeting highlighted how much Iran is out of step with the rest of the region over Syria. Other major rebel backers at the conference included Gulf states led by Iran rival Saudi Arabia.
"The bloodshed in Syria is the responsibility of all of us and will not stop until there is real intervention to stop it. The Syrian crisis is bleeding our hearts," Morsi told delegates at the 120-nation Nonaligned Movement, a Cold War-era group of mostly developing nations that Tehran seeks to transform into a powerful bloc to challenge Western influence.
A major effort by Iran has been trying to showcase its nuclear narrative and cementing oil deals and trade with Asia and Africa to offset the hits from Western sanctions.
But some critics question whether the group promoted as a third way for developing nations during the decades of Washington-Moscow brinksmanship is too diverse and splintered by too many divisions, such as Syria, to find any common policies.
"Morsi's comments violated the traditions of the summit and are considered interference in Syrian internal affairs," said Syrian Foreign Minister Walid al-Moallem, who headed the Syrian delegation. He also accused Morsi of "instigating bloodshed in Syria," according to quotes reported by the state-owned Al-Ikhbariya TV. He didn't elaborate.
Morsi's address pushed Iran further into a corner. In effect, he demanded Iran join the growing anti-Assad consensus or risk deeper estrangement from Egypt and other regional heavyweights such as Turkey and Saudi Arabia.
State Department spokesman Patrick Ventrell welcomed Morsi's comments on Syria as "very clear and very strong," particularly as they were made in Tehran "to some people who need to hear it there."
"We share Egypt's goal to see an end to the Assad regime, and an end to the bloodshed, and a transition to a democratic Syria that respects human rights," Ventrell told a news conference in Washington.
Ahram Online, a state-owned news website in Egypt, said Morsi "all but equated the Assad regime with the Israeli occupation of Palestine when he referred to the struggle for freedom by the Palestinian and Syrian peoples."
Morsi has proposed that Iran take part in a four-nation contact group that would include Egypt, Turkey and Saudi Arabia to mediate an end to the Syrian crisis. Ban also said Iran has a key role to play in finding a solution to end Syria's civil war, which activists say has claimed at least 20,000 lives.
But Syrian rebels say they reject Iran's participation in any peace efforts.
Morsi reiterated his position against any kind of foreign military intervention in Syria, but is working closely with countries such as Turkey and Saudi Arabia that have openly backed the rebel forces.
Morsi held talks on Syria with Ahmadinejad in a closed-door meeting that lasted 40 minutes in the same conference center where the summit was taking place, diplomats said. He told Ahmadinejad that Tehran must end its support for Assad in order prevent any chance of Western intervention, according to the diplomats who spoke on condition of anonymity because they were not authorized to talk to reporters.
At the United Nations, Turkey's Foreign Minister Ahmet Davutoglu was expected to urge the Security Council later Thursday to set up a zone in Syria to protect thousands fleeing the civil war. But the initiative is almost certain to meet resistance from Council members such as Russia, which has supported the Assad dynasty for decades.
"We should all express our full support to the struggle of those who are demanding freedom and justice in Syria and translate our sympathies into a clear political vision that supports peaceful transfer (of power) to a democratic system," Morsi said.
He added that the world had a "moral duty" to stand with the Syrian people in their struggle "against an oppressive regime that has lost its legitimacy."
Morsi's Sunni Muslim Brotherhood backers Egypt's most powerful political group since the Arab Spring uprising that brought down Hosni Mubarak oppose Shiite Iran's staunch backing of the Syrian regime. Assad is a member of the Alawite sect, an offshoot of Shiite Islam, while rebel forces are mostly Sunni.
Iran's state media generally avoided direct mention of Morsi's comments on Syria. The official news agency IRNA did not immediately note the remarks in its report. State TV broadcast Morsi's speech, delivered in Arabic, but did not translate it into Farsi. Another channel has only sporadic translations.
Despite the strong remarks on Syria, Morsi's visit represents a major step toward ending decades of friction between the two countries. Tehran cut ties following the 1979 Islamic Revolution because of Egypt's peace treaty with Israel. A street in Tehran is even named after the ringleader of the 1981 assassination of Egypt's President Anwar Sadat.
Morsi made it clear his six-hour stop in Tehran was intended as an ice-breaker. He referred to Iran's President Mahmoud Ahmadinejad as "my dear brother" and paid homage to "the sister Islamic Republic of Iran" significant departures from the bitter rhetoric of the Mubarak era.
"His visit signifies that Iran is an important regional power that cannot be ignored," said Mohamed Abbas Nagi, an Iranian affairs analyst at Cairo's Ahram Center for Political and Strategic Studies.
"However, Morsi's rise came out of Egypt's own revolution, so how can Egypt pursue better ties with Iran now when that country is suppressing a revolution in Syria?" added Nagi, noting that Egypt's immediate priority appears to be restoring relations with Saudi Arabia and other wealthy Gulf states that were close to Mubarak.
Morsi also gave a nod to Iran by stressing the rights of countries to develop nuclear energy for peaceful purposes under international protocols. The West fears Iran's uranium enrichment could lead to atomic weapons, but Iran has insisted that it only seeks reactors for energy and medical purposes.
The U.N. chief called Iran's nuclear program a "top concern" of the international community and urged Tehran's "full cooperation" with the U.N.'s International Atomic Energy Agency, which seeks greater access to Iranian sites for inspections. The IAEA said Thursday that Iran has effectively shut down a probe of its Parchin military site southeast of Tehran believed to have been used for work on nuclear weapons.
Ban also urged all parties apparently including Israel to "stop provocative and inflammatory threats; a war of words can quickly spiral into war of violence."
But he added specific censure for Iranian condemnations of Israel. Earlier this month, Iran's Supreme Leader Ayatollah Ali Khamenei said Israel will "disappear from the scene of geography." In his speech Thursday, Ahmadinejad called Israel a "fake regime."
"I strongly reject threats by any member states to destroy another or outrageous attempt to deny historical facts such as the Holocaust, claiming that another state, Israel, does not have the right to exist or describing it in racist terms," Ban said.
Aaron David Miller, a scholar at Princeton's Woodrow Wilson Center and former Mideast negotiator under four U.S. presidents, described Morsi's first major foreign policy foray as a deft balancing act before his scheduled trip to the U.S. next month.
"He loses points with the U.S. by going to Iran, but he balances that by criticizing Syria and, by extension, Tehran," he said, adding: "He split the difference as far as the U.S. is concerned, and that's a smart play."