Advancing overnight, troops north and south of the Badiya desert area met up and seized Jabal Dahek, said the Syrian Observatory for Human Rights.
By encircling them, the government forces dealt a "strategic" blow to the IS jihadists, said the Britain-based Observatory.
They have been battling for months to retake the Badiya, which stretches from the country's centre to the Iraqi and Jordanian borders and has been held by IS since 2014.
Fighting was still raging between the two sides near Sukhnah, one of the main towns in the desert area.
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The jihadists have long surrounded government forces in the province's capital city, also named Deir Ezzor.
Analysts say the Syrian army needs to completely eliminate IS from the central part of the desert before it can attack Deir Ezzor, otherwise its troops would be exposed.
According to Fabrice Balanche, an expert on Syrian geography, the regime would have more than half of the country's territory under its control if it can drive IS out of the Badiya.