Harris, a Democrat, held a 31,483-vote lead entering Monday's count of vote-by-mail, provisional and damaged ballots.
Harris has 4,189,949 votes to Cooley's 4,160,211, or 46 percent versus 45.6 percent, according to figures released by the Secretary of State's Office.
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Harris has led since Friday. Cooley, a Republican, had led from from Nov. 5 until Friday.
When polls closed Nov. 2, Cooley declared victory, but by early Nov. 3, Harris led by almost 15,000 votes.
Under state law, county registrars of voters must complete the vote counting by Nov. 30 and provide their counts to the Secretary of State's Office by Dec. 3.
Harris is trying to become the first woman and first black to be elected as California's attorney general. Cooley is trying to become the only Republican in California to win a statewide election this year.