Some 400 people including IS fighters, relatives and wounded, gave themselves up to an alliance of rebel groups on Tuesday, said a spokesman for the Jaish al-Nasr faction which took part in the operation.
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"We hit them with artillery in the town of Al-Khowein until they agreed to surrender," Abu al-Majd al-Homsi said.
Homsi said the fighters would be interrogated to find out whether they had planted sleeper cells in the area, and would be put on trial in "special courts".
IS once held swathes of northern and central Syria including parts of Hama, Homs and Aleppo provinces and much of Raqa, including its provincial capital.
After a string of major defeats last year, hundreds of IS fighters fled to a pocket of territory at the intersection of Hama, Idlib, and Aleppo provinces.
They have now been fully ousted from all three, according to the Syrian Observatory for Human Rights.
Syrian government troops pushed them out of Hama and into Idlib province last week, Observatory head Rami Abdel Rahman said.
"Around 250 fighters with their families, or 400 people in total, were besieged in Al-Khowein," Abdel Rahman said.
"Now, Idlib, Hama, and Aleppo are completely clear of IS."
IS fighters are still present in smaller numbers in the provinces of Homs, Deir Ezzor, Hasakeh, as well as around Damascus and in Syria's south.
IS operated an Islamic "governorate" in Idlib over four years ago, but it was kicked out of the province in early 2014 by Islamist fighters and allied rebels, only returning after a blistering series of defeats late last year.
The Islamist and rebel fighters went on to oust the regime from the rest of the province in 2015 but are now facing a ferocious government assault aimed at retaking key territory there.
Announcing the IS surrender on Tuesday, rebels accused Syria's government of having granted the jihadists safe passage into Al-Khowein.
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