The remains of a new dad killed at the World Trade Center on 9/11 have finally been identified more than two decades later — thanks to groundbreaking new DNA technology.

John Ballantine Niven, 44, of Oyster Bay, Long Island, was on the 105th floor of the South Tower when he was killed on that fateful Tuesday — leaving behind his wife and 18-month-old son.

The new father was the senior vice president of mergers and acquisitions at Aon Risk Services.

His remains have been positively identified using breakthrough DNA sequencing technology, along with a mitochondrial DNA analysis and other procedures that have been refined since the 2001 terror attack, New York City officials announced Thursday.

“It certainly emotional for me to hear 23 years later that John’s DNA has been found.” Niven’s widow, Ellen, told The Post.

“We had no idea those efforts were still underway,” she said of the technology that led to John’s identification.

“Especially given how many years have passed, we are all the more appreciative of the city of New York and the devoted teams working behind the scenes all this time. They deserve tremendous credit for this extraordinary effort.”

Niven is the 1,650th victim identified from the deadliest act of terrorism on American soil, when hijackers crashed airplanes into the Twin Towers, killing 2,753 people.

Ellen said she is grateful that the family will have a part of him to lay to rest.

“We have a gravesite where we buried a box of mementos, and will now be able to bury part of him, which is meaningful for us,” she told Newsday.

Niven, Ellen and their young son lived together in an Upper East Side apartment, but would flock to Long Island on the weekends, according to an online obituary.

He was described as a caring father who went everywhere with his boy, also named John.

In his free time, Niven liked to read philosophy and history books, and play tennis with his childhood friends.

He attended Lake Forest College in Illinois and was a member of the St. Nicholas Society of New York.

Following Niven’s heartbreaking death, his wife said he “would say that although his life was short, he was really blessed in the years he had.”

The younger John Niven, now 23, also lauded the efforts to find his father’s remains.

“As I was, like so many, too young to remember the events of 9/11, it means so much to see how New Yorkers have stayed true to the ‘Never Forget’ promise,” he told The Post.

“The medical examiner’s office and the police who continue to deliver this emotional news are doing incredible work, and the enduring effort of these tributes is even more moving given the considerable passage of time,” he added.

Another 1,103 victims at Ground Zero have not yet been identified, but the Medical Examiner’s Office is hoping this new technology will drastically help.

It allows for specific fragments of DNA to be plucked from a larger, often deteriorated sample to be analyzed.

It was recently used to connect Gilgo Beach murder suspect Rex Heuermann with some hair found on victims’ bodies.

“Our solemn promise to find answers for families using the latest advances in science stands as strong today as in the immediate days of the World Trade Center attacks,” Chief Medical Examiner Jason Graham said in a statement.

“This new identification attests to our agency’s unwavering commitment and the determination of our scientists.”

Mayor Eric Adams also said in a statement: “While the pain from the enormous losses on September 11 will never leave us, the possibility of new identification can offer solace to the families of the victims.”

The Medical Examiner’s Office previously announced in September it had also identified the remains of a man and woman, but their names were not made public at the request of the family.