Two officers from the security services were also killed in the shoot-out in Abyan, a poor and mountainous southern province of Yemen, the government said.
Homeiqani was among a group of 23 militants who tunnelled out of a Sanaa jail in February 2006.
At least 16 of the escapees have been killed or arrested, or have surrendered to authorities.
It is believed that seven fugitives are still on the run.
The escaped prisoners included the leaders of the 2000 bombing of the US warship Cole and the 2002 attack on the French supertanker Limburg.
The jailbreak embarrassed Yemen's government, which is battling Islamist militants, and raised questions about Yemen's security force, many of whom are believed to sympathise with al-Qaeda's ideology.