The charity co-founder was accused of human trafficking and sexually abusing children, but human rights groups called the charges bogus.
Supporters cheered as Ms Hijazi, 30, her husband and six others were found not guilty.
The high-profile case caused concern in Washington at the highest levels of the Obama and Trump administrations.
Activists who have been campaigning for the group's release said the arrests were symptomatic of Egypt's crackdown on civil society.
The prosecution claimed Ms Hijazi and her colleagues had abused their positions while working with Cairo street children.
During the trial, the defence argued that evidence had been tampered with.
The defendants sang as they left the courthouse for a prison vehicle, which was waiting to take them to their final days in detention, according to news agency AFP.
The verdict came less than two weeks after Egyptian President Abdul Fattah al-Sisi met US President Donald Trump in Washington.
Ms Hijazi's relatives said senior US officials told them the case had been raised during the visit, according to the New York Times.
It is not known if it was discussed in the face-to-face meeting between the two leaders.
Ms Hijazi grew up in Virginia in the US, but held dual citizenship and moved to Cairo to work with street children when she left university.
She was arrested, alongside her husband, Mohamed Hassanein, and colleagues from the Beladi Foundation, in May 2014.
US-Egyptian charity worker Aya Hijazi has been acquitted by a court in Egypt after almost three years in prison.