"Staffers felt the horrendous events of that day made it difficult to fully savor one of the country's highest honors for journalistic achievement," the paper said on Wednesday. "And splitting the monetary award among those who had participated in the news coverage just didn’t seem right."
The $15,000 in prize money will go toward repairing the synagogue, which reportedly still has damage from bullets fired during the shooting.
In April, the paper won the Pulitzer Prize for breaking news after reporting on the mass shooting, which left 11 people dead.
The Tree of Life attack was one in a string of recent mass shootings. It came just months before another attack on a synagogue, this one in California. Both attacks reinvigorated calls for gun control and refocused the discussion on extremist ideologies fueling violence in the United States.
On Sunday, Executive Editor Keith Burris presented the synagogue with a check and explained the paper's decision in a speech to the congregation.
"Nothing about doing our duty makes us noble or exceptional," Burris said. "But the duty itself was and is noble. Now we share with you another duty: to remember. And to assure that Pittsburgh, the United States, and all the world, remembers."
The paper also announced it would hold an annual symposium to honor the shooting victims and explore "how free speech and free thought can be used to confront hate speech and violence and overcome both with decency and love.”
The Associated Press contributed to this report.