Joseph J. Lhota, the chairman of the transportation authority, pointed out that rebuilding the station had been a complex project, requiring working with other state and city agencies and developers to determine where the new buildings were going to be located before they could even begin to plan subway entrances.

“Remember, there was a lot of construction,” he said. “These entranceways would have been in the middle of construction sites where there were cranes and all of that. Safety is one of the most important things that we deal with every single day here.”

Lower Manhattan has rebounded and thrived in the years since the attack, pulsating with businesses, residences, restaurants and stores, the kind of urban energy that seemed unimaginable in the weeks and months following the death and destruction that unfolded over several terrible hours on that September day. The return of the subway station underscores the rebirth.

The No. 1 train has bypassed the station for years. On Sept. 11, part of the route collapsed under the avalanche of falling debris.

Shortly after the attack, John Ferrelli, the chief of infrastructure for the subways, assessed the damage: “We basically had dozens of floors of a huge building falling from 600 feet right on top of our roof. It was like a pile driver.”

The new station is a rare piece of good news at a time when the subway is in crisis, with seemingly constant delays more than a year after Gov. Andrew M. Cuomo declared the system to be in a state of emergency. Mr. Cuomo did not attend a brief ribbon-cutting ceremony Saturday, but was instead campaigning ahead of the Democratic primary on Thursday. His office declined to give an explanation for why the governor did not attend the subway opening.