The royal chatted to an elderly woman who acts as a living testament to the horrors of the Second World War and teaches children about her experiences.
The 26-year-old Prince outraged Jews worldwide in 2005 when he was photographed at a fancy dress party wearing a swastika armband and a badge of the German Wehrmacht, or defence force, on his collar.
At the time, the Simon Wiesenthal Centre, one of the largest international Jewish human rights organisations, called on the Prince to visit the Auschwitz death camp to learn about the atrocities committed by the Nazis.
Within hours of the picture being published in a national newspaper, Clarence House issued a statement from the Prince in which he apologised for any offence.
The Memorial to the Murdered Jews of Europe is a striking modern monument of 2,711 "concrete stelae" designed by architect Peter Eisenman and arranged in a grid pattern that visitors can walk through.
The towering slabs were covered in snow today as temperatures in the German capital plunged to minus 12C as the Arctic chill continued to grip Europe.
Harry spent some time walking through the monument, which has proved a big draw to all who visit Berlin, but spent much of his time in an information centre below the landmark which was opened early for the visit.
The atmospheric space has low lighting and features the letters, pictures and images of those who were transported to concentration camps and later killed.
The Prince met the unidentified elderly woman, who is thought to have recounted her experiences to Harry, and he also spoke to staff from the institution.
The Prince also visited another important German landmark – the last remaining section of the infamous Berlin Wall that contains the central "death strip".
The historic section of the barrier is part of the Berlin Wall Memorial dedicated to commemorating those who lost their lives attempting to flee the Communist regime.
Harry was taken up to a viewing tower were he looked down on the preserved site complete with a watchtower.
Before leaving, the Prince left a wreath of cream roses at a simple Window of Remembrance in an open space covered in snow which was 12 inches deep.
A short note penned by the Prince read: "For all those who have paid the ultimate sacrifice in the pursuit of freedom."
On the last day of his two-day trip to Berlin, Harry also visited the world famous Brandenburg Gate. The late 18th-century monument was commissioned by King Frederick William II of Prussia as a symbol of peace.
The Prince arrived in Berlin on Saturday to attend the televised fundraising gala – Ein Herz fur Kinder (A Heart for Children) run by the national German newspaper Bild.
During the event, which raised more than 13m for good causes, Harry received a "Golden Heart" award in recognition of his charity work in Lesotho.