The officials said he was injured in a US airstrike last week and then died subsequently, though they wouldn't say how they know he is dead.
The initial US assessment was that he was "likely killed" in the strike, but further assessments led them to understand he had been injured and only later died.
He was killed along with 12 additional Daesh militants in a wave of strikes by drones and manned aircraft.
Since then, CNN has learned that Shishani was at a "shura," or meeting with other officials, at the time of the strike. US officials had emphasized at the time it was publicly announced that they were not certain of his death and were assessing whether the strike killed him.
One reason the US initially thought Shishani had been killed is that intercepts of his communications had gone silent, CNN learned.
But this situation was a bit unusual, coming together quicker than most. The strike was quickly called in, one official said, when there was sudden intelligence that Shishani was at the meeting. The aircraft and drones had already been patrolling in the skies.
US officials said Shishani had traveled to the al-Shaddadi area from Daesh' unofficial capital of Raqqa to meet with troops in the region who had been in heavy combat and suffered losses.
Shishani has had a reputation as one of Daesh' most capable commanders. There has been a $5 million reward on his head from the US State Department. Also known as Omar "the Chechen" al-Shishani, he was born Tarkhan Tayumurazovich Batirashvili and once served in an elite Georgian military unit.
Shishani joined Daesh in 2013, a US official said, and later was in charge of a prison near Raqqa where the terror organization might have held foreign hostages.
Shishani instructed the group to transport vehicles and weapons to Syria from Iraq in June 2014, and he was eventually named Daesh' northern commander by leader Abu Bakr al-Baghdadi, overseeing military operations in northern Syria, the defense official said.