The planes took off Saturday from Kharkiv, a government-controlled city where the bodies have been brought from the crash site in territory held by pro-Russian separatists fighting the Ukrainian government.
US and Ukrainian officials say the plane was shot down by a missile from rebel territory, likely by mistake.
Officials said the flights took the last of the victims that have been brought to Kharkiv.
International observers have said there are still remains at the crash site. Access has been limited due to rebel interference and security concerns.