It said the information will be shared with lawyers representing the victims' families. It is unclear if the person's identity will become public, BBC wrote.
Fifteen of the 19 Al-Qaeda hijackers who staged the attacks were Saudis.
In 2004, the 9/11 commission set up by Congress found no evidence that the Saudi government funded Al-Qaeda.
However, a 2012 report by the Federal Bureau of Investigation (FBI) said the agency was investigating Fahad al-Thumairy and Omar Ahmed al-Bayoumi, Saudi nationals who had allegedly helped the attackers.
Al-Thumairy is a former Saudi Consulate official, and Al-Bayoumi was once suspected of being a Saudi intelligence officer, according to the Washington Post.
The FBI report, which was released in a redacted form, also referred to a third person. But the name was blacked out.
The victims' families suing the Saudi government have been demanding the identity of that person be released.
On September 11, 2001, attackers flew planes they had seized into New York's World Trade Center and the Pentagon in Washington, D.C. Another hijacked plane was brought down in a field in Pennsylvania.
Saudi Arabia has always denied any connection with the hijackers.
On Thursday, the department said the decision to unmask the name of the Saudi official was taken by Attorney General William Barr.
It said Barr had decided not to invoke state secrets, and share the person's identity with the attorneys for the victims' families.
"The FBI recognizes the need and desire of victims' families to understand what happened to their loved ones and to hold those responsible accountable," the Department of Justice said.
The attorneys for the victims' families have said the unnamed individual is likely a more senior Saudi official than the two people named in the 2012 FBI report.
The victims' families welcomed the decision by the Department of Justice.
"The families are dedicated to getting to the truth, and we shouldn't have to beg for this sort of basic information, or be kept in the dark, about the Saudi role in the attacks," Terry Strada, a member the 9/11 Families and Survivors United for Justice Against Terrorism, was quoted as saying by the AFP.