The unprecedented move drew a furious reaction from Netanyahu, who denounced it as anti-Semitic and the court's accusations "absurd and false".
Israel's closest allies, including the United States, also slammed the warrants against the Israeli politicians, but rights groups including Amnesty International welcomed them.
"Prime Minister Netanyahu is now officially a wanted man," said Amnesty Secretary General Agnes Callamard.
The ICC's move theoretically limits the movement of Netanyahu, as any of the court's 124 national members would be obliged to arrest him on their territory.
"The Chamber issued warrants of arrest for two individuals, Mr Benjamin Netanyahu and Mr Yoav Gallant, for crimes against humanity and war crimes committed from at least 8 October 2023 until at least 20 May 2024," the ICC said in a statement.
A warrant had also been issued for Deif, it added.
Israel said in early August it had killed Deif in an air strike in southern Gaza in July, but Hamas has not confirmed his death.
The court said it had issued the arrest warrant as the prosecutor had not been able to determine whether or not Deif was dead.
The court's chief prosecutor Karim Khan urged the body's members to act on the warrants, and for non-members to work together for "upholding international law".
"I appeal to all States Parties to live up to their commitment... by respecting and complying with these judicial orders," Khan said in a statement.
The Palestinian Authority and militant group Hamas both welcomed the warrants -- though without mentioning Deif.
The warrants for the Israeli leaders are "an important step towards justice and can lead to redress for the victims in general", Hamas's political bureau member Bassem Naim said.
"But it remains limited and symbolic if it is not supported by all means by all countries around the world."
- 'Reasonable grounds' -
The court said it had found "reasonable grounds" to believe Netanyahu and Gallant bore "criminal responsibility" for the war crime of starvation as a method of warfare, as well as the crimes against humanity of murder, persecution, and other inhumane acts.
The ICC said the pair were also criminally responsible "for the war crime of intentionally directing an attack against the civilian population".
The court alleged both men "intentionally and knowingly deprived the civilian population in Gaza of objects indispensable to their survival", including food, water, medicine, fuel, and electricity.
Regarding the war crime of starvation, it said the manufactured shortages "created conditions of life calculated to bring about the destruction of part of the civilian population in Gaza".
This resulted in civilian deaths including of children, due to malnutrition and dehydration, the court charged.
It said it had not yet determined if "all elements of the crime against humanity of extermination were met," the court said.
However, judges did say there were reasonable grounds to believe that the crime against humanity of murder had been committed in relation to these victims.
- 'Deeply concerned' -
Washington denounced the warrants against Israel.
"We remain deeply concerned by the Prosecutor's rush to seek arrest warrants and the troubling process errors that led to this decision," said a National Security Council spokesperson.
"The United States has been clear that the ICC does not have jurisdiction over this matter."
Argentina's president, Javier Milei, also expressed his country's "deep disagreement", arguing it "distorts the spirit of international justice".
Yet Italy said it would be forced to comply with the warrant should the Israeli officials set foot in the country.
While Defence Minister Guido Crosetto said he believed the ICC was "wrong" to put Netanyahu and Gallant on the same level as Hamas, if either "were to come to Italy, we would have to arrest them".
Speaking from Jordan, the European Union's foreign policy chief Josep Borrell noted: "It is not a political decision. It is a decision of a court... of an international court of justice.
"And the decision of the court has to be respected and implemented."
- 'Secret' warrants -
The warrants had initially been classified as "secret" to protect witnesses and safeguard the conduct of the investigations, the court said.
They decided to make the public "since conduct similar to that addressed in the warrant of arrest appears to be ongoing", it added.
"Moreover, the Chamber considers it to be in the interest of victims and their families that they are made aware of the warrants' existence."
ICC prosecutor Khan in May requested the court issue arrest warrants for Netanyahu and Gallant over alleged war crimes and crimes against humanity in Gaza.
Netanyahu sacked Gallant as defence minister on November 5.
Khan initially also sought warrants against other top Hamas leaders on suspicion of war crimes and crimes against humanity.
He had already dropped the application for Ismail Haniyeh, the group's political leader, following his death in an explosion in Tehran.
Khan had also requested warrants against former Hamas leader Yahya Sinwar, who was also killed by the Israeli military in Gaza.
Since Hamas conducted its October 7, 2023 attack, the deadliest in Israeli history, Israel has been fighting a war in Gaza, which the militant group rules.
It was triggered by the assault on Israel by Hamas militants, a cross-border raid that resulted in the deaths of 1,206 people, mostly civilians, according to an AFP tally of Israeli official figures.
The Hamas government's health ministry in the Gaza Strip said Thursday that at least 44,056 people had been killed in more than 13 months of war between Israel and Palestinian militants.
The toll includes 71 deaths in the previous 24 hours, according to the ministry, which said 104,268 people had been wounded in the Gaza Strip since the war began.
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