Assad's national security chief, General Hisham Ikhtiyar, died Friday from wounds sustained in the bombing Wednesday that killed three others, including the defence minister and Assad's brother-in-law.
All were key to the government's efforts to stamp out the insurgency.
"The Damascus blast has indeed shifted the balance of power in favour of the FSA," Issa said on Friday.
The government is pulling its most powerful troops from around the country to reinforce Damascus, which allows rebels to swoop in and take over key areas after the soldiers abandon their positions or leave them only lightly guarded
"The Syrian soldiers have been taking refuge in the tanks, the helicopters, the shelling and nothing else. They don't have control over anything on the ground apart from their immediate area," Issa added.
Syria's unrest began in March 2011 when protests calling for political change met a violent government crackdown.
Many in the opposition have since taken up arms as the conflict has morphed into a civil war that activists say has killed more than 17-thousand people.
The government says more than 4,000 security officers have been killed.