The takeover of Division 17 base came as the UN Commission of Inquiry on Syria said Friday that IS fighters accused of atrocities would be added to a list of war crimes indictees.
In a two-day assault on the base in Raqa province, an IS bastion, the jihadists killed at least 85 soldiers, said the Syrian Observatory for Human Rights.
More than 50 troops were summarily executed, 19 others were killed in a double suicide bombing and at least 16 more died in the assault launched early Thursday.
"Some of the executed troops were beheaded, and their bodies and severed heads put on display in Raqa city," an IS stronghold, he told AFP.
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Video shot by jihadists and distributed on YouTube showed IS fighters apparently inside Division 17 living quarters burning a portrait of Syrian President Bashar al-Assad.
The jihadists also distributed photographs via Twitter of bodies of decapitated soldiers strewn on the pavements and strung onto railings of Raqa city.
Also in northern Syria, 30 troops and pro-regime paramilitary were killed in an overnight ambush in Aleppo province, the Observatory said.
IS, which first emerged in Syria's war in spring 2013, has since imposed its near-total control in Raqa province and Deir Ezzor on the Iraq border.
In June, the jihadist group proclaimed an Islamic "caliphate" straddling Syria and Iraq.
Despite opposition by poorly-armed rebels fighting both the army and IS, the jihadists have made advances in several areas of Syria, whose three-year war has killed more than 170,000 people.