Colonel Abdul-Wahab Azzam was killed after he left al-Dailamy Air Force Base to drive home in the afternoon, said Major Sadik Ali.
Azzam was intercepted by two suspected Al Qaeda attackers riding a motorcycle on a main street, around five km southeast of the air base, Ali said, citing an initial investigative report into the incident.
The Yemeni government has repeatedly blamed militants of the Yemen-based Al Qaeda in the Arabian Peninsula (AQAP) for a series of assassinations against army personnel since last year.
The AQAP has carried out a series of assassinations and suicide attacks against the Yemeni military for revenge.
In August, the AQAP bombed a bus which was carrying air force personnel near the air base in Sanaa, killing at least 12 people and injuring a dozen others.