Kammala jumla mai zuwa: Lokacin da Tarayyar Soviet ta mamaye Lithuania a watan Yunin 1940, Aukštuolis tare da sauran manyan mutane sun gaishe da Vladimir Dekanozov, mataimakin Vyacheslav Molotov, a Filin jirgin saman Kaunas. Ya kasance a Lithuania duk da cewa matarsa ta gudu zuwa Argentina kuma ya yi amfani da alaƙar diflomasiyya don taimaka wa Martynas Yčas ya tsere zuwa Berlin. Bayan karɓar Soviet, Aukštuolis ya rasa aikinsa a ma'aikatar amma tare da shawarar Justas Paleckis (sun yi aiki tare a ofishin jakadancin Lithuania a Riga) ya sami aikin koyar da yaren Rasha a Makarantar Sakandare ta 1 a Panevėžys. Ya kasance daya daga cikin 'yan Lithuania 17,500 da aka tura zuwa Siberia a lokacin
An kore shi a watan Yuni na shekara ta 1941. Tare da wasu fitattun 'yan Lithuania da yawa, gami da tsohon shugaban kasar Aleksandras Stulginskis da minista Stasys Šilingas, Aukštuolis sun ƙare a Kraslag a cikin Krasnoyarsk Krai. A cikin 1942, an sake kama shi da wasu Lithuanians 16 kuma aka zarge su da ayyukan Soviet. NKVD ta ba da shawarar hukuncin kisa, amma hukuncin ƙarshe na shekaru 25 a kurkuku an sanar da shi ne kawai a watan Fabrairun 1952 <unk> kusan shekaru uku bayan mutuwar Aukštuolis daga tarin fuka da rashin abinci mai gina jiki a Dubravlag.