Seven fighters are thought to have died in the clash.
Security checkposts at Khar, the main town in Bajaur, and Siddiqabad, an adjoining village, were also attacked, wounding at least three security personnel.
Hakimullah Mehsud, the Pakistan Taliban chief, remained defiant on Sunday in a telephone call to an AP news agency reporter, threatening to turn Pakistan into "another Afghanistan or Iraq'' unless the Pakistani army's assault against the Taliban stopped.
He said the Taliban had not suffered "any significant losses'' in South Waziristan.
The army began its offensive into this tribal region nine days ago vowing to crush the Pakistani Taliban, which it says is behind 80 per cent of the suicide bombings in Pakistan.
The US backs the operation as they believe fighters in the northwest region are providing shelter to al-Qaida leaders responsible for attacking Nato troops.
The UN said some 155,000 civilians have fled the area beacuse of the fighting.