Aquino's assassination triggered the popular "people power" revolt which later ended the 20-year rule of dictator Ferdinand Marcos as the country's president.
The killing also propelled his widow, Corazon Aquino, to the presidency as the Philippines' first democratically elected president after Marcos.
"After more than 20 years, it's already time because they may only have a few days left in this world. On a personal basis, it's time to move on"
Agapito Aquino, brother of slain opposition leader
Reacting to news of the pardon Benigno Aquino III, a senator and the son of the slain leader, suggested that political revenge may be behind the move to free the men.
"We can't do anything about it because it's the absolute power of the president," he said.
Aquino was shot dead in August 1983, moments after soldiers escorted him from a plane on his return from exile in the US to lead opposition to Marcos's rule.
The men were acquitted in their first trial under Marcos, when the court ruled that Aquino was slain by Rolando Galman, a supposed communist hitman, who was killed by security guards.
Following Marcos' ouster, the country's supreme court nullified the acquittals and ordered a new trial.
In 1987, a court convicted the 16 soldiers of killing both Aquino and Galman, and sentenced them to 40 years in prison.
The trial failed to establish who may have ordered the assassination but speculation has long focused on Marcos, who died in exile in Hawaii in 1989.
Agapito Aquino, a former senator and brother to the murdered senator, said their family has already forgiven the soldiers.
"For me, after more than 20 years, it's already time because they may only have a few days left in this world," he said.
"On a personal basis, it's time to move on."