Chicago mayor Rahm Emanuel held on to his office – and his city career – on Tuesday night beating his rival, Jesus "Chuy" Garcia, in the city's first-ever mayoral runoff.

With nearly all voting precincts reporting results, Emanuel – former chief of staff to Barack Obama – had about 56% of the vote compared to around 44% for Garcia.

"To all the voters, I want to thank you for putting me through my paces," Emanuel told supporters on Tuesday night. "I will be a better mayor because of that. I will carry your voices, your concerns into ... the mayor's office."

Garcia, a Mexican-American county commissioner and former legislator, had been betting on large turnout from both Hispanic and African American voters. Since the first election night 7 February, over 20,000 Chicagoans registered to vote, many in the city's predominately white wards where Emanuel fared well in both election rounds.

Prior to Tuesday's election, a citywide poll had Emanuel leading Garcia by 13 percentage points. An early poll also predicted Garcia would fare poorly among African American voters.

Garcia's loss also marks a defeat for several of the city's largest unions who supported the Mexican-American candidate, including the local branch of the Service Employees International Union and the Chicago Teachers Union, which represents the city's public school workers and which pumped over $300,000 in campaign donations into Garcia's campaign.

The Chicago Teachers Union has decried both the city's nearly $20bn in unpaid pensions and its use of an appointed process to select Chicago Public Schools' Board of Education – a process Emanuel is dead set against changing. When asked if he thinks Emanuel will yield on those issues, civil rights leader the Rev Jesse Jackson Sr – who publicly threw his support behind Garcia – said he "doesn't know".

"The election's over, but the problems are not over," Jackson Sr said on Tuesday night. "The cards are stacked in Rahm Emanuel's favor. But there is no plan for capital development, there's no housing plan, there's no plan for hospitals and construction, so the suffering continues."

Emanuel, who boasted more than $18m in campaign donations, has offered up a Chicago casino as one solution to the city's pension crises. The mayor has also refused to rule out what would be a supremely unpopular property tax increase in order to meet a state-mandated, $550m payment to cover unpaid police and fire pension funds.

Garcia's camp officially conceded at 8.19pm. Just after 9pm, Garcia stepped to the podium with his wife, Evelyn, at his side, at his campaign party on the city's Near West Side. A crowd of around 400 supporters feverishly chanted his name.

One person called out: "We love you, Chuy."

"I love you too," the candidate said, smiling, before telling the crowd he had called to concede to Emanuel, whose name sent the throng of supporters into boos.

"We will not stop fighting for the people," Garcia said to thunderous applause. "Not today, not tomorrow, not ever."

Jesus 'Chuy' Garcia's loss also marks a defeat for several of the city's largest unions. Photograph: Chloe Riley/Guardian