George Pataki ordered the design changes because police were concerned that the tower's placement adjacent to West Street, a major thoroughfare along the west side of Manhattan, would make it vulnerable to a truck bomb.
Instead of being 25 feet from West Street, the tower will be set back 90 feet, and its 200-foot base will be a reinforced concrete wall covered in steel and titanium.
"I think it's simpler and at the same time a lot more elegant," Pataki said in an interview with CNN. "The footprint is smaller, which leads to more open space and it doesn't quite dominate over the memorial ... It's not about doing it today, it's about doing it right for tomorrow."
"The Freedom Tower," will retain the height of the earlier design -- at 1,776 feet, symbolizing the year the United States declared its independence.
But it will also include reminders of the twin towers it will replace.
The roof above the public observation deck will be at 1,362 feet, the height of old South Tower, while a glass wall will rise 1,368 feet, the height of the old North Tower.
"In subtle but important ways this building recalls what we lost," said architect David Childs.
The building will bear a spire that will emit light at night to echo the Statue of Liberty's torch.
The tower will be also more slender and occupy a smaller footprint in the northwest corner of the 16-acre site -- a footprint the same size as the old twin towers' base, 200 feet by 200 feet.
The revised tower design takes up the same amount of commercial space, one-quarter of what was lost on September 11, 2001, and many of the same features.
Above an 80-foot lobby and 120 feet of floors housing mechanical equipment, there will be 69 office floors, the highest at 1,120 feet.
The new construction timetable calls for the steel frame to rise above street level in 2007 and be topped out in 2009, with the tower ready for occupancy in 2010. That's two years later than originally planned.
"The new Freedom Tower design incorporates standards the police department had sought to protect the building against bomb blasts, which our counterterrorism experts agree present one of the greatest threats to such iconic structures," said NYPD Commissioner Ray Kelly, in a written statement.
Real estate developer Larry Silverstein said the tower will have a solid concrete core and state-of-the-art fireproofing on its steel beams.
Silverstein, who leased the Trade Center six weeks before it was destroyed, said he embraced the recommendations of the National Institute of Standards and Technology, which found that the dislodging of fireproofing material when the hijacked planes crashed into the towers contributed greatly to their collapse.
The tower was originally conceived by architect Daniel Libeskind, whose master site plan was chosen in February 2003 to guide the rebuilding process.
Libeskind later was forced to collaborate with Childs, hired by Silverstein, to refine the design, which was unveiled in December 2003.
The 2003 Freedom Tower model featured a torqued glass-and-steel design with a steel cable netting. It had 2.6 million square feet of commercial space, including more than 60 floors for offices, an indoor observation deck above and a sky restaurant to replace Windows of the World.