NFL Commissioner Roger Goodell, 49ers coach Jim Harbaugh, linebacker Patrick Willis and left tackle Joe Staley joined York and others on stage to cut the ribbons.
They used oversized red scissors with gold-colored blades in keeping with team colors. Hard-hat wearing construction workers lined the steps in fluorescent yellow jackets as team employees cheered and a fog horn blared.
"This is a long time in the making," York said.
The stadium's opening put one of the NFL's flagship franchises on firm footing and planted the country's most popular sports league in technology-rich Silicon Valley for the first time.
Goodell called it a milestone for the league. He also added a twist to the ceremony by addressing the looming stadium issue just up the road in Oakland, where the Raiders have long been searching for a replacement to the outdated Coliseum.
Goodell said it's up to the Raiders to decide whether they want to try to build a stadium in Oakland or share the facility at Levi's Stadium with the 49ers an idea York has never dismissed.
Raiders owner Mark Davis has said he doesn't want to be a renter in the 49ers' facility, which is now fitted with red seats and posters of past and present San Francisco greats.
The 49ers' new home, which is the first LEED Gold Certified stadium in the NFL for its environmentally friendly design, will hold about 68,500 fans and has the ability to expand to 75,000 for Super Bowl 50 in February 2016. The facility features 165 luxury suites, 9,000 club seats and even a green roof-top deck that includes solar panels and harvested herbs for on-site food preparation.
Free Wi-Fi will be available at the stadium, and a smartphone application will allow fans to have food delivered to any seat and check waiting lines at concession stands and bathrooms.
"The stadium reflects the greatness of the region, the technology and the innovation," Goodell said.
The seats in the lower bowl will hold some 45,000, or two-thirds of stadium capacity, and will be the largest first level in the NFL.
All club levels look out to the field in one direction and the surrounding valley and mountains in another. It's 35 rows up to the first club seating area, while Row 1 of the stadium is about 10 feet off the field.