As of Wednesday afternoon, Villanueva had 50.2 percent of the vote to McDonnell's 49.8 percent, with all precincts reporting, but provisional and late-mail ballots had yet to be tabulated.
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If Villanueva does win, it would be the first time a sitting L.A. County sheriff has been unseated since 1914.
A spokesperson for Villanueva said they were waiting on the final provisional ballot count and McDonnell had not called to concede. The challenger had a lead of just under 5,000 votes.
Villanueva held a news conference Wednesday and his campaign released celebratory photos after he and his staff saw the latest result numbers.
McDonnell, who raised eight times more in campaign funds than his opponent, was forced into the contest in June when Villanueva did well enough in the primary to force a runoff.
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Villanueva had the endorsement of the union representing rank-and-file deputies and had the backing of the Coalition for Humane Immigrant Rights of Los Angeles, an immigration activism organization. McDonnell's supporters included Los Angeles Mayor Eric Garcetti and county District Attorney Jackie Lacey.
>>>See live midterm election results for Los Angeles County races
Villanueva claimed that McDonnell had failed to reform the department.
McDonnell was elected in 2014, the first outsider to win an election as sheriff in a century. He spent most of his career in the LAPD and was chief of the Long Beach Police Department.