The move will allow the city to begin designing and building the long-delayed school, which is set to serve more than 800 middle schoolers when it opens in 2017.
"Everybody's celebrating," said Community Board 2 Chairman David Gruber.
The building had been occupied by the state's Office for People with Developmental Disabilities, but the state transferred control to the city on Monday.
"Oftentimes in politics you spend a lot of time keeping things from getting worse, so it's nice to be working on something that's really an improvement," said Matt Borden, Assemblywoman Deborah Glick's chief of staff.
The city paid $40 million for the building last year.
"We are excited to begin a process that will result in a new state-of-the-art building for students and families," said DOE spokesman Harry Hartfield.
Some local officials were displeased with the 2017 timeline, saying they had hoped the school could open sooner.
The plans were delayed when the Office for People with Developmental Disabilities couldn't move out because its new home in Lower Manhattan was damaged in Hurricane Sandy, officials said. The projected 2015 opening of the school was pushed to 2016, and now 2017.
"The building at 75 Morton has been cleared and the keys have been turned over to the School Construction Authority," said a spokeswoman for the Office for People with Developmental Disabilities.
In a statement, Gruber insisted the DOE meet the previous 2016 goal.
"This can and must happen," he said.