A boy, 3, and girl, 2, were in an upstairs bedroom at 1116 Baywood Drive and toppled through a window screen, falling onto a bush below in a bark-covered planter area, at about 6:35 p.m.
Family members inside the home's first level did not witness the fall but heard the children's crying outside the front door, according to the fire department.
Petaluma fire paramedics assessed the children's injuries, and because of the distance of the toddlers' fall, the children were transported to hospitals.
The girl was airlifted to Children's Hospital and Research Center in Oakland, and the boy was transported by ambulance to Santa Rosa Memorial Hospital.
As of 8:40 p.m., the extent of the children's injuries was unknown, according to the fire department.
Police also responded to the scene.