The Council approved the override on Thursday by a 46-5 vote.
The controversial legislation requires direct recipients of at least $1 million in city subsidies to pay their workers at least $10 an hour plus benefits, or $11.50 without benefits.
Bloomberg has said he would sue if the council overturned his objection.
The bill is expected to go into effect in 90 days.
Also on Thursday, the City Council voted to approve a $68.5 billion budget for the next fiscal year that avoids tax hikes and major layoffs and restores funds for child care programs.
Prior to the vote, Council Speaker Christine Quinn called the budget a "victory for families of all different incomes."