The couple, who was accompanied by a guard and no child, booked a hydroplane to visit Ha Long Bay on Sunday, VnExpress reported.
The pilot said he only knew that there would be VIP guests flying from Bra to Ha Long Bay and that he was requested not to turn back to talk to the guests.
After returning to Hanoi, the couple visited the Old Quarter and several tourist destinations before leaving on December 22.
This was the fourth time the Hollywood stars have visited Vietnam since 2006.
Jolie came to Vietnam for the second time in 2007 when she adopted a Vietnamese child, Pax Thien.
The third time was in 2011 when they took their children to visit Con Dao Islands in southern Vietnam.
Jolie is now in Cambodia with their six children to direct the highly anticipated "First They Killed My Father: A Daughter of Cambodia." Her adopted sons, Maddox, who was born in Cambodia, and Pax Thien, will be among the actors in the film.
Pitt visited his family in Cambodia last week when they were spotted at a night market in Siem Riep.