Harris has 4,203,346 votes to Cooley's 4,172,616, or 46 percent versus 45.6 percent, according to figures released by the Secretary of State's Office.
Harris, a Democrat, held a 29,738-vote lead entering Wednesday's count of vote-by-mail, provisional and damaged ballots.
There were 89,624 ballots processed Wednesday, reducing the number of uncounted ballots to 671,594 -- 249,002 vote-by-mail ballots, 378,854 provisional ballots and 43,738 that are either damaged, could not be machine- read and need to be remade and ballots diverted by optical scanners for further review, according to the Secretary of State's Office.
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.