Speaking at Walter Payton College Prep school in Chicago after the vote, Emanuel said he was pleased by the outcome.
"This settlement is an honest compromise," he said. "It means a new day and a new direction for Chicago public schools."
Lewis led the walkout on Sept. 10, the first Chicago teachers' strike in 25 years, to protest Emanuel's demand for sweeping education reforms. Some 350,000 public school students were affected by the largest U.S. labor dispute in a year.
Emanuel on Monday tried to get a court order ending the strike, angering the union. A court hearing on his request is scheduled for Wednesday.
The strike focused attention on a national debate over how to improve failing schools. Emanuel, backed by a powerful reform movement, believes poorly performing schools should be closed and reopened with new staff or converted to "charter" schools that often are non-union and run by private groups.
Teachers want more resources put into neighborhood public schools to help them succeed. Chicago teachers say many of their students live in poor and crime-ridden areas and this affects their learning. More than 80 percent of public school students qualify for free meals based on low family incomes.
Only about 60 percent of Chicago students graduate from high school, far below the national average of 75 percent and more than 90 percent in some affluent Chicago suburbs.
The decision by the union to walk out of classrooms eight days ago rather than accept Emanuel's reforms galvanized the weakened U.S. labor movement after a string of national defeats.