Dr Moaiya Hassanain of the Palestinian health ministry in Gaza said that six police officers and an 11-year-old girl were also among the dead after several hours of fighting outside Moussa's home and the Ibn Taymiya mosque where he was imam.
Hassanain said that 150 people were wounded in the fighting.
Hamas also confirmed the death in the fighting of Abu-Jibril Shimali, a high-level commander whom Israel says orchestrated the capture of Gilad Shalit, an Israeli soldier still being held in the Gaza Strip.
The fighting began on Friday after Moussa proclaimed "the creation of an Islamic emirate in the Gaza Strip" during a sermon in the mosque and called for the territory to be governed purely by sharia (Islamic law).
Hamas security officials blocked all roads to Rafah and declared the town a closed military zone as they battled about 100 of his supporters.
At least 40 members of the group have been arrested, according to the interior ministry, but search operations continued in Rafah on Saturday evening.
"We hold Jund Ansar Allah and Moussa responsible for what happened because of his rash declaration of an emirate," Taher al-Nono, a spokesman for the Hamas government in Gaza, said.
Ayman Mohyeldin, Al Jazeera's correspondent in Rafah, said Jund Ansar Allah subscribed to a "very radical and strict interpretation" that is commonly referred to as Salafism.
"It's really the ideological force behind many of these attacks we've seen in Afghanistan and elsewhere," Mohyeldin said.
"It really divides the Muslim world from the Christian and Western world and believes that there is a direct clash of civilisations.
"This group here in Gaza sees itself as part of that wider conflict.
"They subscribe to that philosophy, calling on their followers to adopt it in their struggle to end both Israel's occupation and the occupation of all Muslim lands at the hands of Western powers."
Ghazi Hamad, a senior Hamas official, told Al Jazeera that Moussa's group had little support among the Palestinian people.
"I think these people are a very small group and have no strong impact on people," he said.
"What has happened has confirmed the reality that Hamas is different, Hamas is not al-Qaeda"
expert on political Islam
"Hamas is a wide organisation in Palestinian society and most people in Gaza are moderate people ... but these people are inspired by small groups, radical groups from outside, I think they are not accepted by Palestinian people."
Hamas, whose surprise election win in 2006 led to international sanctions, seized control of the Gaza Strip in 2007 after forcing out security forces loyal to Mahmoud Abbas, the Palestinian president.
In the West Bank, Saeb Erekat, an aide to Abbas and a senior figure in the rival Fatah movement, said that the situation in the Gaza Strip was "alarming".
"Gaza is going down the drain in chaos and lawlessness," he said.
Diaa Rashwan, an expert on political Islam at the Al-Ahram Centre for Political and Strategic Studies in Cairo, told Al Jazeera that pressure on Hamas had "opened the door" for such groups to establish a power base in the territory.
"Such Islamic groups are criticising Hamas, because of the way it negotiates ... and the way it accepted democracy and accepted elections," he said.
"What has happened has confirmed the reality that Hamas is different, Hamas is not al-Qaeda. We have deep differences between Hamas's methods and al-Qaeda or Salafist jihadist methods."