The 2013 budget for the Chicago Transit Authority was unanimously approved by the Chicago Transit Board on Tuesday.

The budget, totally $1.39 billion, was the product of a mass transit system trying to balance scarce revenues with substantial increases in ridership. The CTA said ridership has increased 5.4 percent in the past 19 months.

The transit agency said the new budget maintains current service levels and freezes base fares. But it comes on the heels of eliminating 12 bus routes and a fare increase on monthly and weekly passes, both of which were points of consternation among commuters.

The CTA said the moves were necessary to eliminate a projected $165 million deficit.

“The Chicago Transit Board supports this responsible, sound budget, which includes solid management practices and strategies,” said Chicago Transit Board Chairman Terry Peterson.

The CTA cited three major components of the budget that allowed for additional savings: a “historic” labor agreement with two major unions, supply and management reforms – and “modest price changes to its fare passes.”

The labor agreement with the CTA’s largest unions, the Amalgamated Transit Union Locals #241 and #308, represented a deal with more than 7,000 bus and rail operators.

The CTA said the four-year, tentative agreement “slows the rate of growth in health-care spending” and is estimated to save $50 million. Additional agreements with other unions netted an another $10 million.

The Board held two public hearings on the budget in December, where many voiced concern about the changes, especially the elimination of 12 bus routes, which the CTA said was necessary to increase service to more crowded bus and rail routes as part of its much-touted “decrowding plan.”

The elimination of the #11 Lincoln bus route was a particular point of ire among senior citizen groups and 47th ward Alderman Ameya Pawar, who called the route a “lifeline” to his ward.

“Seniors, and many other vulnerable population ride this bus to get to and from stores and access critical services in my neighborhood,” Pawar told WBEZ in an interview last week. “This is at the top of a one size fits all plan that was made in a vacuum.”

CTA spokesman Brian Steele told WBEZ last week that the other buses axed only serve about 2 percent of CTA commuters.

The CTA has also repeatedly defended the increases to the fare passes, estimated to generate an additional 10 percent of revenue, saying the normal base fares remain unchanged at $2 for bus and $2.25 for rail, and that the increases were keeping in line with other major cities.

“Under the leadership of Mayor Rahm Emanuel, our goal has been to once and for all fix the CTA’s troubled finances; modernize our infrastructure; and protect our bus and rail service, as well as the jobs that provide it,” said CTA president Forrest Claypool. “This fiscally responsible budget moves us away from the past legacy of ‘doomsday’ budgets that have had dreadful consequences for our customers. We are moving forward and building a modern CTA that better serves customers and creates economic benefits for our region.”

Despite the more controversial elements of the budget, the CTA offered some bright spots for customers.

A proposed $5 fare on transit trips originating from the O’Hare Blue Line station, which was meant to target tourists, was altered after reviewing public feedback.

The CTA said the O’Hare fare, a product of a $2.75 surcharge, would be mitigated for employees working at the airport.

“Until that system is developed, the Board approved a temporary solution through July 1, 2013 that will exempt all riders using Chicago Card or Chicago Card Plus cards from paying the full $5 fare, giving airport workers more options to avoid the surcharge that is intended primarily for visitors and infrequent users,” the CTA said in a statement.

The budget announcement also made note of an effort to modernize the system and upgrade its aging infrastructure, at the cost of $2 billion.

“The 2013-2017 Capital Improvement Program (CIP) totals $2.8 billion, with projects designed to modernize aging CTA infrastructure, overhaul and replace fleet vehicles, and bring the system into a state of good repair,” the CTA said.

—Judith Ruiz-Branch contributed to this report.