The court ruled that the documents confirmed by the Russian authorities in Crimea and Sevastopol "have no legal effect in Lithuania and cannot be legalized".
In the ruling issued in late February, Judge Danguole Martinaviciene said Crimea's annexation took place in violation of Ukraine's territorial integrity and international law.
The female defendant whose identity is not disclosed to the media had asked Lithuanian institutions to recognize the divorce decision made by a Crimean judge earlier this year.
Vilnius Registrar's Office rejected her application, stating that decisions made in Crimea have no legal effect in Lithuania. But Vilnius City Court refused to give her divorce under a separate procedure and turned to the Court of Appeal of a clarification.
The latter ruled that the registrar's office acted correctly by refusing to accept the Crimea-issued document, and it also called the actions of the district court legally incorrect.
Russia occupied and annexed Ukraine's Crimea Peninsula in 2014, leading to sanctions from the West and the blacklisting of businesses and people linked to the Russian administration in Crimea, their asset freezes and bans for them to travel to the European Union.