In a stage-managed breakthrough, attended by some 200 dignitaries 30 km inside the tunnel and broadcast live on Swiss television, engineers from both sides shook hands after the bore had pummelled through the final 1.5 metres of rock.
"Here, in the heart of the Swiss Alps, one of the biggest environmental projects on the continent has become reality," said Swiss Transport Minister Moritz Leuenberger.
"By drilling this tunnel, we are participating in the construction of European infrastructure," he said.
Tunnel workers paid tribute to their colleagues who had died on the construction site with a minute's silence as the names of the eight victims were read out during an emotional ceremony for the breakthrough.
"Workers, thank you, thank you, thank you. We have not only built a tunnel, we have written history," said Luzi Gruber, of the construction company Implenia.
The 57 Km high-speed rail link, which will open in 2017, will form the lynchpin of a new rail network between northern and southeastern Europe and help ease congestion and pollution in the Swiss Alps.
It is the third tunnel to be built through the snowbound St Gotthard area but it is much the longest and three Km longer than a rail link between two Japanese islands, the current record holder at 53.8 Km.
"The myth of the Gotthard has been broken for a third time. Our forefathers struggled from the Middle Ages onwards to make this mountain passable," Peter Fueglistaler, director of the Federal Transport office, told journalists gathered for the final breakthrough.
The breakthrough was also watched by a European Union transport ministers at a meeting in Luxembourg.
Passengers will ultimately be able to speed from the Italian city of Milan to Zurich in less than three hours and further north into Germany, cutting the journey time by an hour.
But the 9.8 billion Swiss franc (7.0 billion euro) tunnel, which is 9.5 metres in diameter, is also the fruit of strong popular wave of environmental concern about pollution in the Swiss Alps with booming road traffic transiting from neighbouring countries.