After the fall of Baku to the Azerbaijani-Turkish Army of Islam as result of the Battle of Baku, he fled to Krasnovodsk. On September 20, 1918, he was one of the 26 Baku Commissars shot by the local government of the Socialist Revolutionary Party. His legacy appreciated highly in the Soviet Union as well as in the Soviet republics of Caucasus. However, after the collapse of the Soviet Union the places named after Dzhaparidze in Azerbaijan were renamed and his monument was demolished. His grave was also relocated along with the other commissars in Baku, which was strongly opposed by the Azerbaijan Communist Party and other local left-wing politicians. In his native Georgia, the name of Dzhaparidze is also almost removed from everywhere.