The 6.1 magnitude quake occurred along the same fault as the disastrous May 12 temblor, which killed up to 87,000 people.
The Xinhua news agency reports most of the fatalities occurred in Sichuan's worst-hit county of Huili, where 27 people were reported dead, 321 injured and more than 45,000 made homeless by the quake.
The Ministry of Civil Affairs said on its website that 152,000 people were evacuated to safer housing after the quake wrecked approximately 258,000 houses in the two provinces.
The strong shaking seriously damaged reservoirs, bridges and other facilities, according to Xinhua. Electricity, roads and communications were cut off due to earthquake damage in several rural areas of Yunnan and Sichuan.
The State Seismological Bureau said it had recorded hundreds of aftershocks since the initial quake struck at 4:30 p.m. Beijing Time on Saturday afternoon.
