The $8.7 billion budget was approved by a vote of 45 to 5.
The council was expected to sign off on the advertising arch across Clark by Wrigley Field and a new contract with the police sergeants.
Aldermen also considered a new ordinance on e-cigarettes, aimed at curbing youth smoking, but did not vote on it.
Users of electronic cigarettes could soon find themselves subject to Chicago's smoking ban as the city tries to limit the use of the battery-powered nicotine vapor inhalers, which have become popular among minors and young adults.
Emanuel is backing an ordinance that would expand the city's regulation of tobacco products to include e-cigarettes, barring their use in offices, indoor public areas and within 10 feet of building entrances.
Electronic cigarettes are metal or plastic battery-powered devices resembling traditional cigarettes that heat a liquid nicotine solution, creating vapor that users inhale. Users get nicotine without the chemicals, tar or odor of regular cigarettes. But their popularity among young people has raised the concern of public health officials and lawmakers.
Authorities in Illinois and other states have accused manufactures of marketing e-cigarettes to children, and Gov. Pat Quinn signed legislation in August that will ban their sale to minors in Illinois starting Jan. 1. More than 20 other states have done the same.
Chicago's crackdown is paired with another ordinance to be introduced next week that would prohibit the sale of menthol and flavored tobacco products within 500 feet of Chicago schools.
"This is part of our overall strategy to address the impact of tobacco on youth," city Health Commissioner Dr. Bechara Choucair told the Sun-Times. "We've seen a decrease (in youth smoking), then a plateau. We really need to break that plateau."
Based on survey results released in September, the Centers for Disease Control and Prevention estimated that nearly 1.8 million middle and high school students had tried e-cigarettes in 2012, mirroring increases in the use of the product by adults.
That helped prompt Illinois Attorney General Lisa Madigan and several dozen of her counterparts from other states to call on the U.S. Food and Drug Administration to ban the sale of e-cigarettes to minors and regulate ingredients and advertising.
In Chicago, Emanuel's approved 2014 budget includes an increase on cigarette taxes of 50 cents a pack (instead of the initially proposed 75 cents), which gives the city the highest combined state and local tax in the country.
The ordinance on menthol and flavored tobacco products would expand the school zones where sales are outlawed by five times.
"We know that adolescent smokers use flavored products," Choucair said. "That's how Big Tobacco gets these kids addicted. They lure them in with these colorful packing and sweet flavors."
The Associated Press contributed to this report.