The agency said Monday that ash stopped falling on a swathe of the capital around 3 a.m. (0800 GMT).
The activity began late Sunday afternoon. Mexico City residents awoke Monday to cars coated in a light dusting of ash.
Sunday night winds were carrying water vapor, gas and ash in a west-northwesterly direction.
The agency's monitoring cameras showed glowing rocks shot from the volcano's crater landing more than a half-mile (1,000 meters) down its slope.
About 25 million people live within 62 miles (100 kilometers) from the crater of the 17,797-foot (5,426-metre) stratovolcano.
It's been periodically erupting since 1994.
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