South Waziristan is a tribal area considered to be a base for fighters linked to al-Qaeda and the Taliban.
Pakistan has deployed security forces throughout the northwest of the country in an attempt to combat opposition fighters, but soldiers are the frequent target of attacks.
Petraeus's trip signals Pakistan's crucial role in Washington's "war on terror", particularly in the escalating war in neighbouring Afghanistan.
But it also comes amid tensions over suspected American missile strikes in Pakistan.
Sunday's attack came two days after 12 alleged fighters were killed by two missiles fired by a suspected US drone near Wana.
That raid followed an attack in neighbouring North Waziristan, where two missiles killed 20 suspected Arab fighters, including al-Qaeda's propaganda chief, security officials said.
Washington had offered $1m for the death or capture of Abu Jihad al-Masri, an Egyptian.
Several suicide attacks have come after suspected US air raids or Pakistani military activity to target al-Qaeda and Taliban-linked fighters.
On Friday, at least eight people were killed in a suicide bomb attack outside the house of a senior police official in Mardan, a town lying between Peshawar and the restive Swat valley.
The previous day, Pakistani troops in the northwest of the country had killed five Taliban-linked fighters and captured an explosives expert thought to have links with Afghan opposition fighters.