Alan Fisher, Al Jazeera's correspondent in Bern, the Swiss capital, said: "There is concern in Switzerland undoubtedly about what is being seen as the spread of radical Islam, but the Muslim community here has always been regarded as fairly moderate.
"They were saying that they wanted to see this proposal defeated, so I'm sure it is a real shock to them that at the moment we are seeing that most of the people here have voted in favour of [the ban]."
After the official results were known, far-right politicians celebrated, while the government sought to assure the Muslim minority that a ban on minarets was "not a rejection of the Muslim community, religion or culture".
Eveline Widmer-Schlumpf, Switzerland's justice minister, said the result "reflects fears among the population of Islamic fundamentalist tendencies".
"These concerns have to be taken seriously ... However, the Federal Council takes the view that a ban on the construction of new minarets is not a feasible means of countering extremist tendencies," she said.
Farhad Afshar, who heads the Co-ordination of Islamic Organisations in Switzerland, said that "the most painful for us is not the minaret ban, but the symbol sent by this vote."
Supporters of the ban say minarets represent the growth of an alien ideology and legal system that have no place in the Swiss democracy.
"Forced marriages and other things like cemeteries separating the pure and impure - we don't have that in Switzerland, and we do not want to introduce it," Ulrich Schlueer, co-president of the Initiative Committee to ban minarets, said.
"Therefore, there's no room for minarets in Switzerland."
But Switzerland's Muslims said that the referendum had fuelled anti-Islamic feeling in the country.
"The initiators have achieved something everyone wanted to prevent, and that is to influence and change the relations to Muslims and their social integration in a negative way," Taner Hatipoglu, the president of the Federation of Islamic Organisations in Zurich, said.
"We are frightened, and if the atmosphere continues to be like this and if the anti-Islamic hate increases, then the Muslims indeed will not feel safe anymore. This of course is very unpleasant."
About 400,000 Muslims live in Switzerland, whose population is just under eight million. Most Muslim citizens are immigrants from the former Yugoslavia and Turkey.
Although Islam is the country's second largest religion after Christianity, there are only four mosques with minarets in the whole country.
Posters by those backing the ban showed a figure of a woman shrouded from head to foot in a burka. Behind her is the Swiss flag, shaped like a map of the country, with black minarets shooting up out of it like missiles.
The cities of Basel, Lausanne and Fribourg banned the billboards, saying they painted a "racist, disrespectful and dangerous image" of Islam.
The United Nations Human Rights Committee called the posters discriminatory and said Switzerland would violate international law if it bans minarets.