The bomber, who was wearing an explosives belt, targeted Major General Salem Ali Qatan as he was on his way to work, witnesses said. He was taken to hospital, where he died. A doctor said 12 people, including 9 soldiers, were wounded.
Monday's attack showed that militants have the ability to strike despite losing ground to the army, which regained control of several towns in the southern province of Abyan last week.
Yemeni analysts said the assassination bore the hallmarks of al Qaeda in Yemen, and was probably carried out in revenge for Qatan's role in the army offensive against the militants, which was launched under his supervision.
Islamist fighters, emboldened by weak central government control, went on a rampage in Yemen's south last year while former President Ali Abdullah Saleh was grappling with protests that eventually toppled him.
The United States, alarmed by the apparent strength of al Qaeda-linked group Ansar al-Sharia (Partisans of Islamic Law), has supported the Yemeni army offensive against the militants.