This came a day after both countries placed travel-restrictions on each others' diplomats.
Hours earlier Pakistan had imposed tight restrictions on American diplomats, banning unauthorised travel and stripping them of diplomatic perks.
Colonel Hall is accused of involvement in a road accident in which his vehicle ran a red light and killed a motorcyclist named Ateeq Baig in the capital, Islamabad, on April 7. He was reportedly intoxicated. In fact the matter was also discussed during the last visit of USA official Alice Wells. Mr Hall was involved in a fatal accident and his case is being heard in Islamabad High Court, which the other day declared that he does not enjoy immunity.
The US diplomat was let go by police officials in Islamabad after the accident as the law - Vienna Convention on Diplomatic Relations, 1961 - provided the diplomat immunity from criminal prosecution.
Sources said that a special aircraft had arrived at the Noor Khan Airbase earlier today to fly back the United States diplomat to Washington but the Federal Investigation Authority (FIA) obtained his passport for clearance. The plane returned to Bagram, and Hall returned to the embassy.
A spokeswoman for the State Department confirmed the travel restrictions on Pakistani and American diplomats to the news service, but would not comment on Hall's situation.
A letter sent to the U.S. Embassy in Islamabad says the restrictions will be implemented Friday.
The new U.S. rules require diplomats to obtain permission to travel more than 40 kilometers (25 miles) from their stations, the local Dawn newspaper reported.
The US has complained that the police and security officials in Pakistan often harass American diplomats and their staff with traffic stops and citations that require considerable time and effort to resolve.
The Trump administration has also sought to strengthen ties with India, Pakistan's bitter rival.