Abdul Qayim Patyal was rushed to hospital but died of his injuries there, the official Tawab Ghorzang told AFP.
Kandahar's Mirwaiz hospital also confirmed Patyal's death.
"It is hard to believe that Patyal, the deputy governor of Kandahar province is no longer among us. Rest in peace," Ghorzang said in a tweet.
The last major political assassination in Kandahar occurred in July when a suicide bomber killed Hashmat Karzai, a cousin of the country's last president Hamid Karzai.
