The killing comes a day after the tribal leader met journalists on a trip arranged by the army to show the area had been cleared of rebels.
Witnesses said unidentified assailants on Sunday ambushed the car of former lawmaker Faridullah Khan Wazir close to the Afghan border near Jandola, about 60 km east of South Waziristan's main town of Wana.
Wazir, his driver and a guard were killed on the spot.
Major-General Niaz Khattak, commander of Pakistani forces in South Waziristan, told reporters on Saturday around 100 foreign fighters were hiding in the long tribal belt bordering Afghanistan.
But he said that not a single one was present in South Waziristan.
Meeting with Wazir
The military arranged a trip for Islamabad-based journalists on Saturday to South Waziristan, about 400 km northwest of the capital Islamabad, where they met Wazir and other pro-government tribal elders.
Several pro-government tribesmen have been killed in South Waziristan since security forces launched a series of operations to flush out Muslim fighters from the rugged region in March last.
More than 300 rebels were killed and 700 captured while 250 army troops were killed in this campaign, officials say.
Pakistan has waged a campaign to root out rebels including senior figures linked to al-Qaida that are believed to be holed up in the rugged terrain of the country's tribal region, which borders Afghanistan.