Speaking to foreign ministers from nations in the International Security Assistance Force in Afghanistan, Clinton hailed their "heroic sacrifices" and played down the July date set by President Barack Obama to start withdrawing US troops.
"We need to ensure that these sacrifices are not overtaken by political expediency and short-term thinking," Clinton told the meeting in Berlin.
"We need to worry less about how fast we can leave and more about how we can help the Afghan people build on the gains of the past 15 months," she said.
Obama has tripled US troops in Afghanistan to around 100,000 since taking office in 2009 but had promised to begin a drawdown in July 2011. The nearly
10-year-old war has become unpopular with US voters, particularly Obama's base.
But Clinton insisted that the military campaign was producing gains, pointing to President Hamid Karzai's March announcement that Afghan forces would assume security in key areas including the southern province of Helmand.
"For the transition to be sustainable and irreversible, and for reconciliation and diplomacy to bear fruit, we must sustain our efforts," Clinton said, according to her prepared remarks.
"We need to underscore that we are transitioning, not leaving," she said, stressing that the transition was only in its infancy.
Despite public opposition in the United States and allied nations, Obama's Republican political foes have attacked him over the July deadline, saying it sent the wrong signal to the Taliban and neighbouring Pakistan.
The Obama administration has gradually walked back from the timeframe,
instead stressing 2014 as the date when most US forces would leave.
Clinton appeared to de-emphasise that timeframe as well, saying that the United States was committed to "building an enduring partnership with Afghanistan that will last well beyond 2014."
"The Taliban need to know that they cannot wait us out," Clinton said.
She warned of a "violent spring fighting season" in Afghanistan as the bitter winter comes to a close and the Taliban try to exert themselves in areas where Afghan forces will assume control.
"We have to steel ourselves and our publics for the possibility that the Taliban will resort to the most destructive and sensational attacks we have seen," she said.