"My message to the women and men of Afghanistan is clear: go to the polls," Rasmussen said, wrapping up a two-day NATO foreign ministers' meeting at alliance headquarters in Brussels.
"Only you have the right to decide your country's future," he said.
Hours earlier, a Taliban suicide bomber blew himself up at the Afghan interior ministry, killing six police officers just three days before the country's presidential election.
Rasmussen condemned the attack, but welcomed "that the Afghan people have resisted these intimidation attempts".
More From This Section
The attack came as the three leading candidates to succeed President Hamid Karzai made a final push for votes with rallies on the last day of campaigning.
Kabul has been rocked by a string of high-profile attacks in the run-up to Saturday's election, which will be the first democratic handover of power in Afghanistan's turbulent history.
But despite the violence and a Taliban strategy "to make headlines", Rasmussen said "the overall level of violence today is lower than at any time in the last two years".
While all remaining 53,000 NATO combat troops will depart by December, a small US force may be deployed from 2015 on counter-terrorism and training operations if the next president signs a security deal with Washington.
Rasmussen said without the deal, there would be no international presence to succeed the NATO mission.