A senior White House official said that Trump never directly told Netanyahu to prohibit the visit but that advisers conveyed the president's views to the Israeli government after it initially said the women would be allowed in.
Netanyahu "was certainly aware of the president's position," the official said.
Like others, the official spoke on the condition of anonymity to discuss sensitive deliberations.
The president's advisers have given him mixed views on how to deal with "the Squad" - Omar, Tlaib and Representatives Ayanna Pressley and Alexandria Ocasio-Cortez.
Some Trump aides have told the president to particularly focus on Omar and Tlaib because they are the most polarizing - and poll the worst - in the eyes of his campaign advisers.
Other US officials worried that Trump's opposition to their travel would backfire, one official said. Trump dismissed those arguments, saying Omar and Tlaib's criticisms of Israel make them worthy targets.
But some Republican critics of the congresswomen broke with Trump and Netanyahu, saying the decision was wrong.
"Denying them entry into #Israel is a mistake," tweeted Sen. Marco Rubio. "Being blocked is what they really hoped for all along in order to bolster their attacks against the Jewish state."
The American Israel Public Affairs Committee, a powerful pro-Israel lobbying organization that rarely criticizes the Israeli government, said the congresswomen should be allowed to visit. AIPAC said in a tweet that it disagreed with Omar and Tlaib's support for the Boycott, Divestment and Sanctions movement, better known as BDS, which calls for boycotting Israeli goods and services to protest Israeli treatment of Palestinians. But the group added, "We also believe every member of Congress should be able to visit and experience our democratic ally Israel firsthand."
Tlaib and Omar have repeatedly denied harboring animus toward Jews or Israelis and have said their criticisms of the Israeli government are based on serious policy differences.
In a statement, Omar said the Israeli decision was not a surprise coming from Netanyahu, "who has consistently resisted peace efforts, restricted the freedom of movement of Palestinians, limited public knowledge of the brutal realities of the occupation and aligned himself with Islamophobes like Donald Trump."
The leading liberal presidential primary candidates swiftly condemned the decision, with Senator Bernie Sanders, calling it a "sign of enormous disrespect to these elected leaders" and Senator Elizabeth Warren, warning that it would be a "shameful, unprecedented move."
Netanyahu insisted that his government continues to respect the US Congress but said there are limits to whom it will allow entry. "As a vibrant and free democracy, Israel is open to all its critics and criticism, with one exception: Israeli law prohibits the entry of people who call and operate to boycott Israel," he said in a statement.
Senior Democrats in Congress said they felt particularly misled by Israel's ambassador to the United States, Ron Dermer, who said last month that the two congresswomen would be allowed to visit Israel "out of respect for the US Congress and the great alliance between Israel and America." On Wednesday, Israeli officials notified Democrats that Netanyahu had changed his mind, sparking a last-minute lobbying campaign by Democrats to reverse the decision.
Several Jewish Democrats who have long been critical of Tlaib and Omar's positions on Israel pleaded with Dermer on their colleagues' behalf. Representatives Nita Lowey, Josh Gottheimer, and Eliot Engel - all strong supporters of Israel - phoned the envoy to lobby against barring the congresswomen. Hoyer took the lead on negotiating for the Democrats, but a Wednesday phone call with Netanyahu proved unsuccessful.
While some Democrats said privately that the move exposes Netanyahu as a pawn of Trump, Jewish House Democrats in particular worry that the move will empower critics of Israel, fueling the BDS movement. In phone calls with lawmakers, Dermer tried to justify the decision, saying Omar and Tlaib had no real intention of visiting Israel. Hoyer rejected that view in his statement, saying the decision is "outrageous, regardless of their itinerary or their views."
Now Democrats fret privately that the ban will trigger new tensions between their party and Israel that Trump could exploit. According to one top lawmaker involved in the talks, the party plans to try to use public pressure in the coming days to change Israel's mind about barring the congresswomen.
"I am saddened by the Israeli government's decision to bar two sitting Members of Congress from entering Israel, especially following Ambassador Dermer's public announcement that both women would be allowed to enter just a short time ago," Lowey said in a statement. By blocking them, the Israeli government is "empowering those who seek to create a wedge between our two countries," she added.
With three weeks to go before a repeat election on Sept. 17, Netanyahu is fighting a bitter battle to stay in office and wants to appear strong to his fractured right-wing base.
Omar and Tlaib's trip to Jerusalem and the West Bank was planned by Miftah, a nonprofit organization headed by Palestinian lawmaker and longtime peace negotiator Hanan Ashrawi.
On Thursday, the group called Israel's decision "an affront to the American people and their representatives."
"MIFTAH worked hard to organize a well-rounded visit . . . in order to facilitate their engagement with Palestinian civil society and to provide them with an opportunity to see the reality of occupation for themselves," the group said in a statement. "This is their right and duty as members of Congress, who oversee US policies and actions that affect Palestine, Israel, and countries worldwide."
The question about their entry status arose because of a recently passed Israeli law that denies entry visas to foreign nationals who publicly back or call for any kind of boycott - economic, cultural or academic - against Israel or its West Bank settlements.
Israeli Interior Minister Aryeh Deri, publicly confirming the decision to ban the two lawmakers, said Thursday that the move was coordinated among Netanyahu, Foreign Minister Israel Katz and Minister of Strategic Affairs Gilad Erdan in accordance with the law preventing those who advocate a boycott from entering Israel.
"The State of Israel respects the U.S. Congress, as part of the close alliance, but it is inconceivable that anyone who wishes to harm the State of Israel will be allowed," Deri said in a statement.
Deri made clear that if Tlaib's request to visit included a humanitarian reason - such as a private meeting with her family - then he would consider it.
Trump, who maintains a close relationship with Netanyahu, said last month that the lawmakers should "go back" to the countries they came from, in remarks widely condemned as racist. Tlaib was born in Michigan, and Omar was born in Somalia. Both have criticized Israel's human rights record and treatment of Palestinians.
No official meetings were scheduled for the U.S. lawmakers, but they were planning to travel to the West Bank cities of Bethlehem, Hebron and Ramallah and spend time in Jerusalem.
They were scheduled to meet with Israeli and Palestinian civil society groups, humanitarian workers and young people and see one of the East Jerusalem hospitals affected by recent cuts in US aid to the Palestinians.
