Warren trailed Virginia Sen. Tim Kaine earlier in the day but pulled ahead Wednesday afternoon. The two spent most of Wednesday running neck-and-neck with Kaine holding a slim lead in the CNBC reader poll as they emerged from a field of 12 to turn the contest into a two-person race.
Warren received the most positive votes of any candidate, but trailed Kaine earlier in the day due to the high number of negative votes weighing her down.
Warren has proven to be extremely popular among the party's progressive wing and a potent critic of presumptive Republican nominee Donald Trump, and she'd likely help the presumptive Democratic nominee make inroads with Vermont Sen. Bernie Sanders' voters. Clinton and Warren campaigned together in Ohio on Monday, fueling speculation that Warren could be Clinton's vice presidential pick.
However, Warren could be detrimental to Clinton's efforts to raise money and gain favor with voters in the financial sector.
Kaine, on the other hand, is relatively moderate, and offers Clinton help in winning his swing state of Virginia. He is also a former governor of that state and would be a relatively safe pick.
Trailing Kaine and Warren were New Jersey Sen. Cory Booker, Vice President Joe Biden, Secretary of Housing and Urban Development Julian Castro, Ohio Sen. Sherrod Brown, and Sanders, who traded places throughout voting.
The rest of the list was rounded out by Minnesota Sen. Al Franken, Colorado Gov. John Hickenlooper, Secretary of Agriculture Tom Vilsack, Labor Secretary Tom Perez and California Rep. Xavier Becerra.
Last month, CNBC readers chose former Secretary of State Condoleezza Rice as their top choice for Trump's Vice President. Ohio Gov. John Kasich and former Speaker of the House Newt Gingrich finished second and third in the poll.
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UPDATED: This story was updated to reflect Elizabeth Warren surpassing Tim Kaine in the CNBC polling.
— CNBC's Brian Beers contributed to this report.