The strongest quake registered a magnitude of 7.0 from an epicenter just off the coast of Papua province at a depth of only 18 miles.
The two victims, one a 5-month-old child, were killed when their homes fell in on them on the island of Yapen.
About 500 homes, a church, government buildings and a power plant were destroyed on Yapen, which is located near the epicenter.
Eyewitnesses say the shaking seemed to last for about one to two minutes.
Fear of a resulting tsunami sent many residents fleeing the coast in search of higher ground, but an all clear was issued about an hour after the shaking stopped.