Police say when they questioned Pabon he had scratches on his arms, and bits of flesh containing his DNA were found beneath the victim's fingernails.
A Manhattan judge ordered Pabon held without bail at his arraignment Saturday.
Pabon's lawyer, Mario Gallucci, said his client is innocent. He said the scratches came from either doing yard work or moving, and the DNA samples are inconclusive.
Rodriguez disappeared July 7 in the middle of her shift at the 26-story office building a few hundred feet from ground zero.
The case touched off an exhaustive four-day search by police and raised questions about how she could have vanished from the high-security skyscraper.
Like most office towers in the financial district after the 9/11 attacks, guards staff the lobby 24 hours a day, and cameras cover every exit.
The cameras recorded Rodriguez, 46, when she turned up for work at 5 p.m. and again as she moved around the building, but they never showed her leave. Her last appearance on tape was at about 7 p.m. in an elevator lobby.
Police swept through the building with search dogs in the following days, sure that Rodriguez couldn't have walked out alive.
Finally, they discovered blood leaking from the ventilation shaft; her body was stuffed inside.
An autopsy determined she had been asphyxiated by the tape.
Rodriguez was born in the Dominican Republic, where she will be buried. However, she lived in Manhattan for decades. She was married with several children.
NEW YORK AND TRI-STATE AREA NEWS