Some of those residents had only just returned to their homes after last week's eruptions.
The latest eruption was less powerful, but sent a large plume of dark grey smoke and ash rising from the crater.
Calbuco surprised residents of the Los Lagos region last week by bursting into life after decades of inactivity.
The National Geology and Mines Service issued a red alert after Thursday's eruption, warning that the volcano remained unstable.
On Friday, residents were warned that heavy rain could mix with ash and rock to produce deadly volcanic mudflows.
These "lahars" can slide down volcanoes like avalanches.