Clinton's appeal in Berlin came as President Barack Obama's administration mulled a new strategy for Afghanistan and sought greater European support for defeating Islamist extremists.
"Our history did not end the night the wall came down," Clinton told current and former European and US political heavyweights on the eve of the 20th anniversary of an event that symbolised the end of the Cold War. "It began anew," Clinton said in a key-note speech hosted by the Atlantic Council.
"To expand freedom to more people, we cannot accept that freedom does not belong to all people. We cannot allow oppression defined and justified by religion or tribe to replace that of (communist) ideology," she said.
The chief US diplomat recalled how German Chancellor Angela Merkel, during a visit to Washington last week, spoke of the walls of the last century and "the less visible but equally daunting walls" of today.
"These are walls between the present and the future, walls between modernity and nihilistic attitudes, walls that divide our common heart, that deny progress and opportunity to the many who yearn for both," Clinton said.
Clinton highlighted the moment that Merkel would on Monday walk through the heart of once-divided Berlin as a moment that "should be a call to action, not just a commemoration of past actions.”
"That call should spur us to continue our cooperation and to look for new ways that we can meet the challenges that freedom faces now," Clinton said. "And we need to form an even stronger partnership to bring down the walls of the 21st century and to confront those who hide behind them: the suicide bombers, those who murder and maim girls whose only wish is to go to school.”
Thomas Carothers, an analyst at the Carnegie Endowment for International Peace in Washington said Clinton was echoing the Bush administration in drawing a parallel between the Cold War and the fight against extremism.
"Facing difficult pressures on Afghanistan, the Obama administration marked the 20th anniversary of the fall of the Berlin Wall by revving up a rhetorical trope that President Bush favoured," Carothers told AFP in an email.
"Europeans and others never found it very convincing under Bush," he said. "I suspect they won't like it much better now."
Brent Scowcroft, national security advisor for US president George Bush senior when the Wall fell in 1989, said the North Atlantic Treaty Organization is still looking for a "new strategic concept" after the fall of communism.
In a speech to the same gathering here, he also expressed concern that the transatlantic alliance no longer has "an intimacy of dialogue" that it had in 1989, when Bush consulted frequently with then Chancellor Helmut Kohl.
"It's important that we restore that closeness in order that we all can face in unity the challenges confronting us in a very... difficult world," Scowcroft told the audience.