The Defence Department said Thursday everything was on hold through Sunday except for Saturday's football game against Air Force.
Navy and Air Force received the go-ahead to play because the game is not funded by the government. A sellout crowd is expected.
Army will play its game, too. Boston College said on its website that Saturday's game against the service academy will proceed.
"I'm thrilled our students and those from the service academies will get to play their games this weekend," athletic director Brad Bates said. "Thank you, fans, for your patience and understanding the past couple of days."
Service academy football games are paid for with nonappropriated funds and have been long planned. Such funds generally come from outside sources and are not approved through Congress.
Navy athletic director Chet Gladchuk said his department had provided information to Pentagon officials to assure them that no government money will be spent on any aspect of the game. Gladchuk said a Navy home game brings in about $4 million from tickets, sponsorship, television and radio rights fees and other revenues such as parking and concessions. The game essentially pays for itself, he said.
Football revenue funds Navy's 32 other sports teams.
As for the consequences of a home football game being cancelled, Gladchuk said Wednesday: "It would be devastating to our budget."