A city Department of Transportation worker was killed when a colleague accidentally ran him over with a truck early Tuesday near Gracie Mansion on the Upper East Side, police said.

The victim, a married Queens dad identified as Eduardo Calle-Abril, 44, was standing on East 88th Street near York Avenue at about 1 a.m. during a repaving project when his 35-year-old co-worker inadvertently backed a 2005 DOT Mack truck onto him, cops said.

Authorities found an unconscious Calle-Abril with trauma about the body.

Medics rushed him to NewYork-Presbyterian/Weill Cornell Medical Center, where he was pronounced dead, police said.

“The whole family is heartbroken right now,” Calle-Abril’s younger sister, Andreina Cortez, told The Post Tuesday.

Calle-Abril, whose job title was listed as an assistant city highway repairer, according to records, had a teenage daughter and was from Ecuador, Cortez said.

Mike Donovan, 63, a superintendent of an East 88th Street building near where the fatal incident happened said he heard someone “yelling for 911” when the tragedy struck.

“Suddenly the noise of the trucks stopped, and you heard desperate screams,” said Donovan, who then ran out of his apartment.

“By the time I put my clothes on and went outside, they were taking the worker into the ambulance and FDNY were calling Code Red,” he said, noting that there were roughly 20 people on the scene at the time.

Donovan said he heard one worker shouting “because of you the kids won’t have a father” at the 35-year-old who backed the truck onto Calle-Abril.

“The cops had to pull him back and say, ‘you aren’t helping,’” Donovan recalled. “The guy who ran him over was just in complete shock. You know he’s sorry.”

Upper East Side resident Patrick Kirkley also witnessed the chaotic aftermath during a late-night jog near Gracie Mansion.

“I asked one of the workers what happened. They said he got ran over and he was dead,” said Kirkley, adding, “I feel for the family. I can’t imagine getting that phone call in the middle of the night.”

By Tuesday morning, mourners had formed a makeshift memorial of candles and bouquets on the sidewalk near where the tragedy occurred.

“I feel sad. It’s depressing,” said John Genovese, 21, a worker in a building across the street. “People are irresponsible in New York. Running over your coworker? You can’t just think you’re the only person in this world who’s around.”

A neighbor and pal of Calle-Abril’s showed up at the scene Tuesday to mourn him.

“He was a great friend. He always helped out,” said Maria Torres. “He was so active, participated in all activities. He played soccer…I just can’t believe it happened.”

The driver of the DOT truck was questioned by police, but investigators said there was no criminality, and the incident appeared to be an accident, according to the NYPD.

Neighbors on the block said that the DOT had stripped the street’s pavement two weeks ago and that workers started to pave the roadway starting at around 9 p.m. Monday night.

A DOT spokesman said that the agency is “investigating the circumstances of this tragedy.”

Additional reporting by David Meyer and Yaron Steinbuch