The case received public backlash when it became public that the team's visa applications to travel to the U.S. for an global robotics competition were denied twice.
"We are very happy to have these young girls be able to come here to the United States to participate in this robotics competition", Nauert said.
President Trump's daughter, Ivanka Trump, has welcomed this initiative and she said "I look forward to welcoming this brilliant team of Afghan girls, and their competitors, to Washington DC next week!"
After hearing about the girls' case, Trump asked officials at the National Security Council to assist in the matter, and they in turn consulted the State Department and the Department of Homeland Security, the senior administration officials told CNN.
"We were not a terrorist group to go to America and scare people", 14-year-old competitor Qaderyan told AFP in Herat before the U-turn.
They will represent their war-torn country among 157 other countries for a science fair at the Constitution Hall in Washington D.C. on Sunday night.More news: Bentley Spain named to Outland Trophy Watch List
Homeland Security Department spokesman David Lapan said Wednesday the U.S. Citizenship and Immigration Services approved a State Department request for six girls from the war-torn country to be allowed in, along with their chaperone, so they can participate in the competition.
The U.S. State Department had declined to comment on why the Afghan team's visa applications were denied, saying that "all visa applications are adjudicated on a case-by-case basis in accordance with U.S. law".
The girls wanted to show the world that Afghans could also construct a hand-made robot and they had been deeply disappointed by the initial rejections.
Organizer Ali Reza Mehraban of the Digital Citizen Foundation said the decision meant "supporting peace and women of Afghanistan, who have been deprived of everything for the past forty years".
"I truly believe our greatest power is the power to convene nations, to bring people together in the pursuit of a common goal and prove that our similarities greatly outweigh our differences", said Joe Sestak, president of First Global. Sestak said the State Department was a "star player" in the entire process of coordinating travel for the competing teams, but he had no direct knowledge of Trump's involvement.
Members of the Afghan robotics team on their arrival at Hamid Karzai International Airport. Gambia's team, which designed a robot to clean contaminated rivers, also faced visa problems but was permitted last week to travel to the U.S. Afghanistan isn't one of the six countries targeted by President Trump's travel ban.
Speaking at the airport Thursday, another team member Rodaba Noori said: "This support by the U.S president means support for us and for all women in Afghanistan".