Speaking where the Cold War frontier once split the German city, Kerry said what was left of the Wall served as a reminder that freedoms "are still being threatened in too many parts of the world, and they are even being threatened right here in Europe".
"Russia's aggression in Ukraine needs to end," said Kerry, urging Moscow to honour all aspects of its ceasefire deal with Kiev to end the deadly insurgency by pro-Russian separatists in the east of the former Soviet state.
"We hope Russia -- with whom we do not seek conflict, with whom we would much rather be working together to deal with the problems of the world – we hope that Russia will understand how seriously the world takes the efforts to cross the lines of sovereignty and independence of a nation."
Kerry, who spent part of his childhood in divided Berlin as a diplomat's son, had earlier toured the Berlin Wall Memorial which features a 220-metre (720-foot) section of what was once a 150-kilometre (100-mile) concrete cordon encircling West Berlin.
It is located at Bernauer Strasse, where the Wall sliced through an inner-city neighbourhood, separating families and friends from 1961 until 1989, and leaving house windows and doors bricked up and a local subway stop turned into a ghost station.
The street saw dramatic scenes as residents tried to flee the Soviet sector, sliding down ropes and jumping from windows into the rescue nets of West Berlin firefighters. Later dozens crawled through escape tunnels dug below the Wall and its adjoining mine-littered and electrified "death strip".
Kerry's host, Foreign Minister Frank-Walter Steinmeier, recalled that the Berlin section of the Wall claimed at least 138 lives, mostly of men who were shot or killed by mines as they tried to flee.
Steinmeier said historians had launched a new study into how many lives were lost along the entire Wall dividing the country, to research whether the toll could have been "600, 700 or even 1,000 dead".
'Hope and despair'
Kerry said he felt deeply moved to return to Berlin decades on, and shortly before Germany on November 9 marks a quarter-century since people power brought down the German part of the Iron Curtain.
In a brief German-language address to a press conference, he praised the allies' "long history of cooperation for freedom, peace and prosperity", then went on to recall the time when as a child he took a brief glimpse at life in the communist-ruled East.
"I was 12 years old at the time, very curious about East Berlin, and I exercised the privileges of a diplomatic passport to one day ride my bicycle through the checkpoint into East Berlin," he said.
"I felt the difference, I actually noticed it, and it frightened me enough that I turned back fairly quickly to come back into the American sector. It was a difference between hope and despair, between light and darkness.
"You noticed it in the absence of people, and the colour of the clothing, in the atmosphere. It was the difference also obviously between freedom and oppression - people who were given a chance to make something of their lives and people who were denied that chance."