The board had ruled that variances were not required.
The plaintiffs, who included the alumni group and assorted architects and preservationists, disagreed with the board. They also contended that the Massachusetts Historical Commission is required to review the plans for the entire project as a result of the state Architectural Access Board's ruling.
The judge's ruling, however, emphatically rejected the alumni group's claims.
"The plaintiffs have not shown that there is a likelihood that they would prevail on the merits," Judge Isaac Borenstein wrote in his decision.
"They have also not shown that they would be irreparably harmed if the injunction is not granted nor that any harm the plaintiffs might suffer outweighs the harm to the defendants," he added.
Knowles and Donin were particularly pleased that Borenstein had judged that the University was conscious of its duty to preserve its architectural heritage.
"Although the changes to the Great Hall will be extensive, Harvard has taken steps to protect the historically and architecturally significant features of the building," Borenstein wrote.
The judge pointed to Harvard's consultations with the Cambridge Historical Commission and the hiring of "noted architectural preservation firm" Goody, Clancy & Associates as evidence of Harvard's efforts.
"We believed from the beginning that we had sought and received every necessary approval to carry out this renovation which is so important to academic life of Harvard," Donin said.
Even if it ultimately loses the battle for the Great Hall, members of HAARC said they intend to continue its mission as an oversight committee in the future.
"I think Harvard enjoys a privileged status in the city of Cambridge, in terms of not having all of its historic properties under full jurisdiction of the Cambridge Historical Commission," Webb said. "That is something we would like to look into.