Army ordered to go after Baitullah Mehsud amid market bombing and suspected US missile strike.
The second attack was in a separate village but neither of the officials had details of any casualties.
Frequent attacks by pilotless US drone aircraft have been heavily criticised by Pakistani leaders for killing innocent bystanders and infringing upon national sovereignty.
South Waziristan is part of the federally administered tribal areas which border the North West Frontier Province (NWFP).
The NWFP contains the Swat valley where hundreds of thousands of civilians have fled a government offensive against the Taliban.
The Pakistani military has also been softening up targets in South Waziristan and is expected to launch an offensive against Taliban fighters in the region.