Japanese forces launched a surprise attack on the base in 1941, killing 2,300 US servicemen and propelling the US into World War Two.
Mr Abe will visit on 27 December with US President Barack Obama.
The announcement, two days before the 75th anniversary of the attack, follows a visit by Mr Obama to Hiroshima.
He became the first US president to visit the Japanese city, where about 150,000 people are believed to have been killed in 1945 by a US atomic bomb.
Mr Abe said in a statement: "We must never repeat the tragedy of the war. I would like to send this commitment. At the same time, I would like to send a message of reconciliation between Japan and the US."
The two leaders will pray for the dead at the site of the attack, before a final summit meeting between them in Hawaii.
The White House said the visit would "showcase the power of reconciliation that has turned former adversaries into the closest of allies, united by common interests and shared values".
Mr Abe said: "Our talks in Hawaii will be a chance to show the rest of the world our ever stronger alliance in the future."
The attack on Pearl Harbor will be marked on Wednesday by a remembrance ceremony on a pier overlooking the harbour, where a moment of silence will be held at 07:55 - the time the attack began.