The U.S. Coast Guard on Friday found a whale carcass in San Francisco Bay, but officials quickly determined it was not one of the wayward humpbacks that had swum up the Sacramento River by accident.
A dead California gray whale was found and scientists were expected to perform an autopsy to see if it died of natural causes or a run-in with a vessel.
Whales are a common sight in the open ocean just outside the Golden Gate.
The humpback mother and calf were thought to have slipped back out to sea unnoticed on Tuesday night or early Wednesday.
Thousands of people had traveled to the river and bay to try to catch a glimpse of the pair, dubbed Delta and Dawn.
Biologists said the chance to closely observe them for so long was invaluable for science.
Ariadne Green, 57, of Vallejo, caught a glimpse of the pair on Tuesday and earlier in the week at Rio Vista, where the whales had circled for several days near a bridge. She described the humpbacks' inland visit as a "profound spiritual experience" but was equally grateful for their departure.
Biologists said the saltier water where the mother humpback whale and her calf had been swimming since leaving the Rio Vista area helped reverse some of the health problems caused by long exposure to fresh water.
Recent photographs showed that serious wounds suffered by both whales appeared to be healing, said Rod McInnis, a spokesman for the National Oceanic and Atmospheric Administration. Antibiotics were injected into the whales on Saturday to try to slow the damage from the gashes, likely from a boat's keel.
Lesions that had formed on the humpbacks' skin over the weekend also appeared to be sloughing off.