The presence of the warship, which departed on Thursday, was an "example of the US Navy's commitment to enhancing interoperability at sea, serving as a cornerstone of NATO's military strength, while demonstrating the US and allied forces' capability to provide the right presence, in the right place, at the right time."
Word of the Donald Cook's departure came as Kiev accused Moscow of seeking to trigger a "third world war."
During its stint in the Black Sea, the destroyer carried out exercises with the Romanian navy, as well as with the American frigate USS Taylor.
In an incident that heightened tensions already inflamed by Russia's actions in Ukraine, a Russian fighter jet made a dozen passes at low altitude near the destroyer on April 12.
The Pentagon denounced the move as "provocative and unprofessional."
The US naval presence in the Black Sea will now consist of the USS Taylor, a Navy spokesman confirmed to AFP.
The vessel was deployed to the Black Sea during the Winter Olympics in the Russian resort of Sochi amid concerns about possible terror attacks at the massive international sports event.
However, it had to undergo repairs in the Turkish port of Samsun after running aground there on February 12 as it was preparing to moor. It returned to the Black Sea on Monday.
Earlier this month, Moscow claimed Turkey had allowed the USS Taylor to stay longer in the Black Sea than permitted under international law -- a claim Ankara dismissed.
According to the 1936 Montreux Convention, warships from countries that do not border the Black Sea cannot stay there for more than 21 days.
NJF/NJF