Kamal Hyder, Al Jazeera's correspondent in Islamabad, said that a total of 39 hostages were freed by special forces.
"The attempt was to save as many lives as possible," he said.
"But three hostages died as well two special force soldiers."
Following interrogation of one of the arrested hostage takers by police, Hyder said, there was now evidence that "Dr Uthman" - who is linked to an attack on the Sri Lankan cricket team - was in charge of training the group that carried out the attack.
People in Rawalpindi were less impressed with the storming of the GHQ or the investigation that has begun.
Speaking to Al Jazeera on Sunday, one Rawalpindi resident said: "This is very dangerous. If this happens at army headquarters, despite tight security, then it is going to be tough for ordinary citizens."
Another Pakistani citizen said: "Everyone in Pakistan is at risk. Anyone leaving their house cannot be sure whether he or she will return alive."
The assault on the GHQ began when a group of armed men, dressed as soldiers, attacked the army compound, sparking a gun battle that killed four fighters and six soldiers.
The remaining fighters took hostages, whom Abbas earlier described as security personnel, and barricaded themselves in a nearby office.
The military surrounded the compound and the ensuing siege lasted for more than 18 hours.
It was unclear who was behind the attack, but Rehman Malik, Pakistan's interior minister, pointed the finger at the Taliban.
"We are very sure it was done by the Taliban ... after having their back broken in Swat they wanted to react and they have reacted," he told Al Jazeera on Saturday.
"All this leads to the South Waziristan. Now we have no option except to go into Warizistan."
Malik said that the fighters had spent months planning their assault. "These terrorists had rented a house near Islamabad for the last two months preparing themselves," he said.
"We recovered fuses that are used in suicide jackets from the house."
Speaking to Al Jazeera on Sunday, Imtiaz Gul, a political analyst, also suspected a link between the Rawalpindi attack and South Waziristan.
"A lot of al-Qaeda and ideologically tainted people belonging to the Islamic movement of Uzbekistan under the patronage of the Taliban are sheltering there," he said, referring to South Waziristan.
But not everyone agrees. Zafar Jaspal, a Pakistani analyst, believes that Islamabad has concentrated too much on the Swat valley and South Waziristan.
"Till today, the government has no clear strategy on how to deal with the militants who are residing in southern Punjab," he told Al Jazeera.
"The person who was captured alive after [the GHQ attack] comes from Punjab, and other members of that group are also from Punjab ... certainly the government needs to have a parallel strategy - for Punjab as well as South Waziristan."