The controversial 2.8-billion-franc proposal won the support of 57 percent of voters in Sunday's nationwide referendum.
It was the only proposal to which voters said yes. Three other nationwide referendums - on automatic deportation of foreign criminals, preventing speculation with foodstuffs and tax breaks for married couples were rejected.
Only two of the country's cantons – Geneva and Vaud - rejected the proposal, which will see a second tube built to allow renovation of the existing tunnel.
The canton of Uri, at one end of the tunnel, came out in support of the project despite previously ruling out plans to develop it.
In the canton of Ticino, at the other end, support was stronger, with 76 percent in the commune of Airolo voting for.
The government and proponents had argued that the project was needed to ensure the link between the cantons of Uri and Ticino remained intact while the tunnel built in 1980 is renovated.
They also argued that it would allow the safety of the tunnel to be improved.
Claude Longchamp of the GFS research institute said voters had been won over by these arguments.
Critics had warned that building a second tube would open the door to more truck traffic on the already clogged route that links central Switzerland with northern Italy.
But the government said that after the second bore is completed in around 2030 the two tubes would each carry only one lane of traffic in each direction.
Its policy is to shift as much freight as possible from road to rail.
The Gotthard Base Tunnel for trains which opens later this year will help rail traffic through the Alps.
“[The government] now has to make good on their promises that this is really a renovation of the tunnel and not an increase in its capacity,” Jon Pult, chairman of the Alpine Initiative which opposed the construction, told the Swiss news agency SDA.
Centre-right parties are also concerned that the new tube spells bad news for other road projects.
“Important projects in the agglomerations will be put on hold,” Konrad Graber, a Senate member for the CVP, told SDA.