One rocket hit the southern Israeli city of Sderot, but no casualties were reported. The unrest came amid demonstrations across the Middle East and in the West Bank and Jerusalem.
The biggest turnout, though, appeared to be in the Gaza Strip, where thousands gathered for street protests following midday sermons focused on the United States' decision to move its embassy.
The Israeli military said it had "fired selectively" toward "instigators" of what it described as violent riots at six places along the Gaza border, which it said drew 4,500 participants. "Hits were confirmed," it said. The Gaza Health Ministry said two men were killed.
Fifteen people were injured, including a child, in an airstrike that followed rocket fire from the enclave, the Gaza Health Ministry said. The Israeli military said its jets had targeted a Hamas training compound and ammunition warehouse. It said that one rocket from Gaza was intercepted by Israel's Iron Dome air defense system and that it was trying to identify where another landed.
Rioting broke out in some 30 locations in the Palestinian territories, according to the military, which said 3,000 Palestinians participated in the West Bank. As night fell, the demonstrations had mostly dispersed.
A jihadist group called the Nasser Salahuddin Brigades claimed responsibility for the rocket fire. The Israeli military said it holds Hamas "solely responsible" for all hostilities from the Gaza Strip.
After the airstrike, a third rocket hit Sderot, the military confirmed.
The Islamist movement Hamas, which controls Gaza, had called on its followers to mount a third intifada, or uprising, against Israel after Trump made his announcement Wednesday. Any perceived change to the status of Jerusalem, a city holy to Muslims, Christians and Jews, is contentious.
Speaking in Paris, Secretary of State Rex Tillerson said Trump's decision did not indicate any "final status" for Jerusalem, something that would be left for Israelis and Palestinians to decide. Moving the embassy, meanwhile, "is not something that is going to happen this year," he said. "Probably not next year."
Israeli politicians have widely welcomed the move, but international criticism has mounted, on the grounds that the new policy harms peace efforts. On Friday, the U.N. Security Council held a tense emergency session.
At the meeting, ambassadors from Britain, France, Italy, Japan, China and others on the 15-member body declared Trump's announcement misguided or worse, prompting U.S. Ambassador Nikki Haley to respond that the United States won't be "lectured" about its support for Israel and Middle East peace. The United Nations' envoy to the region, Nickolay Mladenov, said there is a "serious risk" of a chain of unilateral actions that may make peace more distant.
"This is a dangerous precedent that needs reflection," said Amr Abdellatif Aboulatta, the U.N. ambassador for Egypt, the first Arab country to sign a peace treaty with Israel.
For the Palestinians, the real fight may come on the diplomatic front, with officials saying they will make a new push for their own independence and recognition.
Palestinian President Mahmoud Abbas said Friday that Washington has lost its credibility as a broker between Israel and the Palestinians. "With this position, the United States has become no longer qualified to sponsor the peace process," he said without elaborating.
Fathi Hammad, a member of the Hamas political bureau, said at a demonstration in the northern Gaza Strip on Friday: "Today we declare an uprising against the occupation, and there are no half-solutions. We call upon all the free people of the world to boycott America and Israel, and we call on the Arab and Islamic countries to take a serious stand and support our people."
In Jerusalem, demonstrations were limited in scope and dissipated quickly, and some Palestinian residents expressed resignation, along with contempt, about the U.S. move.
Thousands of worshipers prayed at the holy Haram al-Sharif compound, home of the renowned al-Aqsa Mosque, but prayers ended without major incident. Some scuffles broke out between demonstrators and border police near the Austrian Hospice in Jerusalem's Old City, where demonstrators chanted slogans and threw chairs and stones. (Haram al-Sharif, or the Noble Sanctuary, is known to Jews as the Temple Mount.)
Ahmed Aduelhawa, 60, said Palestinians in Jerusalem did not want to give Israel "an excuse to humiliate us," adding that Trump's declaration "doesn't matter." He said: "The future of Jerusalem isn't in Trump's hands, not in Abbas's hands, not in Netanyahu's hands," referring to Israeli Prime Minister Benjamin Netanyahu. "It's in God's hands."
"We usually come on Fridays, but today has special meaning," said Noor Shaheen, 24, as she left prayers. She said the fact that Israeli authorities had not placed restrictions on who could come to prayers on Friday had eased tensions, adding that Palestinians in Jerusalem were weary of protests.
"We are tired," she said. "It's hard to make action without thinking of the reaction."
She said she had been disappointed by what she described as a "weak reaction" by Arab leaders.
In the wider region, battered by bloody conflicts from Iraq to Syria and Yemen, protests lacked intensity, even in countries that have long been vocally critical of Israel. Turkey's president predicted Thursday that the region would ignite in a "ring of fire," but the reality in some places fell short of the rhetoric.
In Cairo, protesters rallied outside al-Azhar mosque, where crowds chanted, "With blood and soul, we sacrifice for you, al-Quds!" using the Arabic name for Jerusalem.
Religious parties, lawyers and trade groups staged protests across Pakistan, burning American flags and effigies of Trump and chanting, "Death to America!" and "Death to Israel!"
But in Lebanon, Hasan Nasrallah, leader of the militant Shiite Hezbollah organization, offered little in the way of concrete support for the Palestinians during an hour-long speech Thursday night. Some in the Hezbollah-dominated Beirut suburb of Dahiyeh said the speech gave voice to a deeper frustration — one that explained why there had not been more protests Friday.
"Why should we fight for them when they have fought us in Syria?" asked 38-year-old Mohamed Ibrahim, an accountant. Palestinians are largely Sunni, and the Shiite Hezbollah has battled Sunni rebels in Syria, in a conflict tinged with sectarianism.
Nasrallah "is not going to war with Israel over the Palestinians," Ibrahim said. "The speech placed the responsibility for what happens next at the door of the Palestinians."
At the Zawiat Dahmani mosque in the Libyan capital, Tripoli, hundreds of worshipers heard the imam, Ali Gadoor, rail against Trump and his decision. He urged those gathered to wage war against Israel. But he also focused his ire on moderate Arab leaders who are key allies of the United States, referring mainly to Saudi Arabia and other Persian Gulf nations.
"How come they are putting dollars in American banks?" Gadoor asked. "Why are they selling oil to the American government? They should withdraw all their dollars from the United States. They should stop selling oil. They need to support the Palestinians."
Gadoor added that he trusts Hamas, which controls Gaza, but no longer has any faith in the Abbas government in the West Bank.
Morris and Eglash reported from Jerusalem. Erin Cunningham in Istanbul; Louisa Loveluck and Suzan Haidamous in Beirut; Sudarsan Raghavan in Tripoli, Libya; Shaiq Hussain in Islamabad, Pakistan; Haq Nawaz Khan in Peshawar, Pakistan; Nisar Mehdi in Karachi, Pakistan; and Anne Gearan in Washington contributed to this report.