Officials say the men had hijacked the aircraft eight hours earlier demanding to go to India. But a Pakistani air force fighter jet intercepted the plane and forced it to land in Pakistan.
The hijackers were identified by the defense ministry as members of a students group that has been protesting reported plans by Pakistan to test nuclear device in their province.
Officials say the hijackers handed over eight of their hostages and were persuaded to leave the aircraft and come out on the tarmac, where they were grabbed by the commandos.
The Pakistan International Airlines plane with 29 passengers and crew members on board was on its way from the remote southwestern Baluchistan province to the southern port city of Karachi when it was hijacked to go to India, officials at Karachi International Airport said.
A Pakistan Air Force fighter jet took off shortly after the hijacking and intercepted the plane, forcing it to land in Hyderabad, about 90 miles from Karachi, the Pakistan Television news broadcast said.
The aircraft was sitting on the tarmac in Hyderabad for hours before commandos were able to coax the hijackers out.
The hijacking came as tensions between Pakistan and India have soared over India's recent testing of five nuclear devices. The two countries have gone to war three times.
Controllers in Karachi informed New Delhi that the plane was heading to India, an Indian air traffic control official said on condition of anonymity. Indian officials feared it could head to Jaisalmer or Jodhpur, both of which are close to Pokaran, the site where India tested the nuclear devices. All airports along the border were activated, he said.
The control tower in Karachi said the plane was coming from Turbat, 240 miles away in Pakistan's desolate southwest along the border with Iran.
By Kathy Gannon