"I am appealing the court's decision because it is not supported by the law, and it undermines important protections that our courts provide to defendants," Harris said in a prepared statement. "This flawed ruling requires appellate review."
Death penalty foes had called on Harris to let Carney's ruling stand rather than risk a reversal in the 9th U.S. Circuit Court of Appeals.
"We hope the 9th Circuit will recognize that California's death penalty system is as broken and unconstitutional as Judge Cormac found," Matt Cherry, executive director of Death Penalty Focus, which seeks to abolish capital punishment, said in response to Harris's move.
Death penalty backers supported Harris' decision.
"It is obviously the correct decision to make," said Kent Scheidegger, the top lawyer at the pro-death penalty Criminal Justice Legal Foundation in Sacramento.
Scheidegger was attending a death penalty conference for government lawyers in San Diego and said the initial ruling by Carney "has been the talk in the hallways" among attendees.
The San Francisco-based 9th Circuit is often viewed as a liberal-leaning court, but the three-judge panel that will consider the appeal by Harris will be randomly selected from the entire court of more than two dozen judges of varying political pedigrees.
"You never know what you're going to get," Scheidegger said of the 9th Circuit's three-judge panels.
Harris has said she personally opposes the death penalty but promised voters she would enforce state law.
Carney's ruling overturned the death sentence of Ernest Dewayne Jones, a Los Angeles man sentenced to die for the 1992 rape and murder of his girlfriend's mother.
Since the current death penalty system was adopted 35 years ago, the judge noted, more than 900 people have been sentenced to death but only 13 have been executed.
The judge called the death penalty an empty promise that violates the Eighth Amendment's protection against cruel and unusual punishment.
"Inordinate and unpredictable delay has resulted in a death penalty system in which very few of the hundreds of individuals sentenced to death have been, or even will be, executed by the state," wrote Carney, a George W. Bush appointee.
He noted that death penalty appeals can last decades and, as a result, most condemned inmates are likely to die of natural causes before their executions are carried out.
No executions have been done in California since 2006 after another federal judge ordered an overhaul of the state's lethal injection procedures.