At the USS Arizona Memorial, President Obama and Prime Minister Abe honoured the 1177 sailors who perished when the ship was bombed on December 7, 1941.
In all, 2400 Americans died in the surprise Japanese attack on Pearl Harbour that drew the United States into World War II.
The day's ceremony is the second in a pair of solemn visits.
Seven months ago President Obama became the first US President to visit Hiroshima, where the US dropped an atomic bomb in 1945 that helped force Japan to surrender. More than 100,000 Japanese were killed.
While there were no apologies, the carefully staged events are intended to strengthen ties between the two countries, and to help close the still lingering wounds of war.
President-elect Donald Trump criticized Japan during the campaign for not paying the US enough for its defence, and even suggesting that Japan develop its own nuclear weapons.
US Ambassador to Japan Caroline Kennedy, who attended the ceremony, was asked if she was concerned about US-Japanese relations during a Trump Presidency.
"I think the alliance is more, is so strong and it has so much bipartisan support - I think President Trump will recognise that," she said.