The high court's decision to dismiss the appeals for lack of jurisdiction occurred as part of a long-running legal battle over California's 33 adult prisons and their often-criticized medical care for inmates.
A panel of three federal judges in August ordered the state's prison population be reduced in stages over two years to relieve the overcrowding that has caused inadequate medical and mental health care.
California's prisons have been filled to nearly twice their designed capacity of 80,000, according to the ruling.
The Supreme Court noted the state has come up with a plan to comply with the lower court's order but the three-judge panel earlier this month put it on hold pending the outcome of the appeals to the high court. With the appeals dismissed, the plan can go forward.
Improving conditions in the nation's largest state prison system has become a major legal, political and budget issue in view of California's budget crisis and high unemployment.