In a narrow decision, investors voted 50.34 percent to 49.66 percent to split the roles of chairman and chief executive. BoA's board unanimously expressed its support for Mr Lewis to continue as CEO.
The revolt against the bank's chief was seen as a protest over its $50 billion takeover of brokerage Merrill Lynch and its continued reliance on emergency government funding.
BoA snapped up Merrill Lynch last September at the height of the market turbulence following the collapse of Lehman Brothers. The bank was subsequently hit by a $15 billion fourth quarter loss for Merrill.
It was also forced to borrow $25 billion under the government's Trouble Asset Relief Program. At the start of this year, the bank asked for a further capital injection of $20 billion, the BBC noted.
Mr Lewis defended BoA's acquisition of Merrill and mortgage lender Countrywide, saying they were "two of the most important reasons BoA is the most profitable financial services company in the United States so far this year".
BoA recorded a net profit of $4.2 billion in the first quarter of 2009.