Abdul Latif Ashna had just left his home and was on his way to his office when a suicide bomber on a motorcycle blew himself up near his vehicle.
One of his bodyguards and his driver were wounded, as were two passers-by in the Afghan town.
Mr Ashna, a trained engineer, had been deputy governor since April 2010.
He previously worked for UN Habitat, the UN programme to improve the urban environment, before teaching at Kandahar University.
Kandahar, the birthplace of Taliban leader Mullah Omar, is at the heart of a nine-year insurgency by the Islamic militants.
Besides foreign troops and Afghan soldiers and police, the Taliban also regularly target local officials whom they accuse of being traitors working with the international forces and the Western-backed Kabul government.
The deputy mayor of Kandahar, Noor Ahmad Nazari, was killed in October, six months after his predecessor was assassinated.
The governor of Kandahar, Tooryalai Wesa, survived a bomb attack on his convoy in November 2009.
"This is the work of enemies of Afghanistan, the Taliban. They kill anyone who is working for Afghanistan's future, to rebuild the country," said Mr Wesa.
Saturday's attack on the deputy governor came a day after a suicide bomber blew himself up in a central Kabul supermarket popular with Westerners, killing at least eight people, including three foreign women.
The Taliban also claimed responsibility for the attack, the first to target foreign civilians in the capital since August 2010.