More from GlobalPost: NATO attack on Pakistan no mistake, sources say
The road to the base was closed Sunday morning and nearby residents instructed not to leave their homes, Pakistan's Dawn news site reported.
An American aircraft then arrived. US personnel, luggage and equipment were loaded on board, according to local TV reports cited by Chinese news agency Xinhua.
Officials from Pakistan's Federal Investigation Agency were reportedly present during the operation.
Neither Pakistani nor American officials have yet commented.
Washington has expressed regret for the soldiers' deaths and opened an investigation into the incident. President Barack Obama will not follow diplomats' advice and issue a formal apology, however, it was reported Thursday.
More from GlobalPost: Pakistan closes US supply routes to Afghanistan, threatening war effort
The US has twice before ignored requests from Pakistan to shut down the Shamsi airbase, the Times of India said. Similar orders were given after a CIA contractor shot two men in Lahore, and following the US military's secret raid in Abbottabad to kill Osama bin Laden.
This time, however, US officials acknowledged that Pakistan appeared more determined to carry out its eviction threat, according to the Express Tribune.
Closing the airbase is considered more of "an inconvenience" than a critical blow to America's drone wars, the Tribune said, citing a government source who told the paper that the US has spent months building up drone launching capacity elsewhere in case it was forced to leave Shamsi.