The 5.4 magnitude temblor struck about 30 miles east-northeast of the Albanian capital of Tirana at 11:49 p.m. local time.
Seismologists say that the very shallow depth of less than 2 miles was responsible for the extent of the damage, which was greater in Albania.
Strong aftershocks continued through Monday, keeping many people from returning to inside their homes.
No injuries or fatalities were reported from the initial jolt or the subsequent aftershocks, officials said.
Electric power and telephone communications were disrupted in many villages and towns in Albania and southwestern Macedonia.
A comparable quake centered in southern Macedonia during late May damaged dozens of homes near the epicenter.