Geneva's residents voted 81.77 percent in favor of bringing back the ban, with only 18.3 percent voting against.
A canton-wide smoking ban in public places was originally introduced on July 1, 2008, after the state government used a first referendum as grounds for pushing through the move.
But the Federal Tribunal ruled three months later that the ban should not have been passed by the canton's lawmakers before the state's government enacted legislation.
The law therefore had no legal basis, the tribunal found.
Geneva's smokers were allowed to light up again at the end of September last year in bars and restaurants following the ruling.
A year on, the smoking ban will once again come into force after the canton's lawmakers passed legislation and had it overwhelmingly approved in Sunday's referendum.
The new rules allow bar, hotel and restaurant owners to fit out special smoking rooms in their establishments, which the original ban did not.
Supporters of the ban are opposed to this compromise, however, and said Sunday they would appeal to the Federal Tribunal.