Just over 50 percent of the electorate backed cutting the fee from 451 to 400 francs, with strongest support for the reduction coming from French-speaking Switzerland and the canton of Graubünden.
Most voters in a majority of German-language cantons voted against the reduced fee, along with those in Italian-speaking Ticino.
The change to federal law on television and radio makes the fee payable by all households, whether or not they have TVs and radios, as well as by large companies.
The legislation aims to reflect the fact many households listen to radio and watch TV on devices such as laptop computers, tablets and smartphones.
People receiving social assistance and residents of group homes will be exempt from the licence fee.
Companies with sales under 500,000 francs will also be exempt from the fee, which it is to take effect in 2018.
Fewer than 4,000 votes separated the yes and no votes in the referendum, with the outcome not immediately evident.
“It has become a Hitchcock thriller,” Communications Minister Doris Leuthard, a proponent of the change told media, as the results came in.
She thanked “yes” voters, saying the change is “positive for three million households”.
Most of the 1.3 billion francs raised annually by the TV and radio licence goes to help finance the Swiss Broadcasting Corporation (SSR) and "public service" broadcasters.
Among other decisions made in national referendums on Sunday, voters soundly rejected a proposed 20 percent national inheritance tax on large estates and legacies.
More than 70 percent of those casting ballots voted against the tax, which would have applied to estates valued at 2.5 million francs or more.
The proposal was backed by left-wing parties as a means to finance the social insurance system.
Cantons and municipalities already levy taxes on inheritance, raising around 900 million francs a year.
The people also voted 72.5 percent against a popular initiative for a standardized national system of student bursaries to replace ones currently providing by the cantons that differ from one part of the country to the other.