While opinion polls indicated that most Swiss were in favour of assisted suicide, they had also suggested that many were against what has become known as suicide tourism.
Many citizens from Germany, France and other nations come to die in Switzerland because the practice remains illegal abroad.
One local organisation, Dignitas, says it has helped more than 1,000 foreigners to take their own lives.
Another group, Exit, will only help those who are permanently resident in the country - saying the process takes time, and much counselling for both patients and relatives.
Its vice-president, Bernhard Sutter, said the result showed Swiss voters believed in "self-determination at the end of life".
The referendum had offered a proposal to limit suicide tourism, by imposing a residency requirement of at least one year in the Zurich area in order to qualify for the service.
It was backed by two conservative political parties, the Evangelical People's Party and the Federal Democratic Union.
But the major parties of the left and right, including the Swiss People's Party and the Social Democratic Party, had called on their supporters to vote against both motions.
The BBC's Imogen Foulkes, in Geneva, says the size of the vote against a ban on assisted suicide reflects the widely held belief among the Swiss that is their individual right to decide when and how to die.
Their rejection of the proposal to limit assisted suicide to those living in Zurich shows that concerns about suicide tourism carry less weight with voters than their conviction that the right to die is universal, our correspondent says.
But the debate in Switzerland will continue, she adds. Polls show voters do want clearer national legislation setting out conditions under which assisted suicide is permitted.
The Swiss government is planning to revise the country's federal laws on assisted suicide.
It has said it is looking to make sure it was used only as a last resort by the terminally ill, and to limit suicide tourism.
Blogger Note: Many ethical issues are found in this story.