Military officials said three hostages were killed in the operation along with at least four hostage takers, one of whom was wearing an explosives belt.
One insurgent has been taken alive and the operation is ongoing as more militants are at large in the compound.
The insurgents had attacked Pakistan's military HQ on Saturday.
Six soldiers and four militants were killed in the initial assault.
'Very skilled'
The sound of blasts and gunfire rang out as Pakistani special forces entered the compound for the pre-dawn raid.
Military spokesman Maj Gen Athar Abbas said the forces had met with resistance.
They found the hostages being held in a room "with a terrorist who was wearing a suicide jacket", he said.
Gen Abbas said the commandos had "acted promptly" and shot the suspected hostage taker "before he could pull the trigger".
"Three of the hostages were killed due to militant firing," Reuters quoted him as saying.
Senior military officials and civilian personnel were reported to be among the hostages.
Gen Abbas said the raid had been a "very skilled rescue" and that security forces were continuing to conduct "mopping up and clearance operations" in the area.
No-one has yet claimed responsibility for Saturday's assault, but the Taliban has been threatening to carry out attacks unless operations against the militant group were stopped.
The militants' attack came as the Pakistani army prepared for a major operation against the Taliban.
High profile
Witnesses said that the gunmen had driven up to the army compound in a white van just before midday local time (0600 GMT) on Saturday.
They took up positions, fired on the compound and threw hand grenades, security officials said.
The military reported that the attack had been repelled after a gun battle lasting around 45 minutes but later admitted hostages had been taken.
The attack followed a series of bombings in north-western Pakistan. On Friday at least 50 died in a blast in Peshawar.
In recent days Taliban positions in the tribal areas have been bombed by the air force, amid speculation that the army's offensive there is soon to be intensified, says the BBC's Aleem Maqbool in Islamabad.
There was a period of relative quiet in August after Taliban leader Baitullah Mehsud was killed, but the rate of militant attacks has increased since then, he adds.
Pakistan's Interior Minister Rehman Malik said the government now had "no other option but to launch an offensive" in the insurgent stronghold of South Waziristan.
"What happened in Peshawar, Islamabad and today, all roads lead to South Waziristan," he said.
Islamist militants have carried out a number of attacks against high-profile, high-security targets in recent years.
In March this year gunmen opened fire on a bus carrying the Sri Lankan cricket team in the city of Lahore. Six policemen and a driver were killed and several of the team were injured.
In the same month, dozens of people were killed when a police training centre on the outskirts of the city was occupied by gunmen.
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