Michael F. Flaherty lost his bid yesterday to win back a seat on the Boston City Council, falling short in his political comeback just two years after appearing as a finalist on the mayoral stage.
Flaherty narrowly missed the fourth at-large seat on the City Council, finishing fewer than 1,000 votes behind incumbent Stephen J. Murphy, according to unofficial results from the city.
“It just wasn’t in the cards today,’’ Flaherty said last night. “We worked hard, and there were a lot of issues we raised in this race.’’
The poor showing by the former City Council president came partially at the hands of Ayanna Pressley. Once deemed vulnerable, Pressley rocketed to the top of the ticket yesterday after receiving the fewest number of votes among the winners two years ago.
Supporters and other elected officials, including Councilor John R. Connolly, rallied behind Pressley, reminding voters that she was the only woman running for reelection and was the first woman of color to serve on the council.
But Pressley also commands extraordinary talent on the stump, winning over crowds with a mix of policy prowess, hard-luck stories of growing up poor in Chicago, and a dose of humor.
“This is more than a little overwhelming,’’ Pressley said last night at her victory party, attended by Governor Deval Patrick. “It’s stunning. It’s humbling.’’
In a surprising finish, all four at-large incumbents - Pressley, Murphy, Connolly, and Felix G. Arroyo - held on to their seats. While at-large elections can be unpredictable, yesterday’s results underscored the power of incumbency.
Flaherty captured 25,790 votes, a far cry from the 46,768 people who voted for him in 2009 when he challenged Mayor Thomas M. Menino. Flaherty gave Menino his strongest challenge to date, but the mayor still won by 15 percentage points.
Flaherty’s defeat represented a victory for Menino’s political operation, which had mobilized a citywide effort to help keep Flaherty from returning to the council.
But Menino’s field organization also suffered a sharp rebuke in Dorchester yesterday. The mayor’s candidate, John K. O’Toole, lost the open seat representing District 3 to Frank Baker.
Boston’s City Council has nine local district seats and four at-large spots that represent the entire city. At-large elections can be volatile because voters can select up to four candidates. Ballot combinations can vary widely, and some enthusiastic supporters will vote for only one person, giving their candidate a bullet vote.
In District 2, Councilor Bill Linehan of South Boston beat back a strong challenge from Suzanne Lee of Chinatown. Councilor Tito Jackson easily kept his seat representing District 7, after besting Sheneal Parker. In District 4 in Mattapan and Dorchester, Councilor Charles C. Yancey won his 15th term, topping his frequent opponent, J.R. Rucker.
In the at-large race, Pressley surged to the top with 37,506 votes. After speculation spread this summer that she was vulnerable, Pressley formed an alliance with Connolly to share resources. They appeared at 25 joint campaign events, sent out joint mailings, and knocked on doors together.
Last night, Pressley talked about her field organization with 500 volunteers, her partnership with Connolly, and cooperation with other elected officials.
“I’m glad that all of my colleagues will be returning,’’ Pressley said.
Arroyo captured second place with 35,465 votes; Connolly, who finished first in the election two years ago, dropped to third yesterday with 32,803 votes; Murphy, the City Council president, grabbed the last seat with 26,712 votes.
“The people of Boston returned us all,’’ Murphy said last night. “I am grateful.’’
Challengers Will Dorcena and Sean H. Ryan both lost with fewer than 10,000 votes.
A product of a powerful political family in South Boston, Flaherty served as a prosecutor for the Suffolk district attorney’s office and waged unsuccessful runs for office. He ultimately won at-large spot on the City Council in 1999 at the age of 30 and held the seat for a decade.
The last time he ran for City Council, he won 25,863 votes in 2007, more than anyone else in the city. But this year, Flaherty ran as a challenger, not an incumbent.
At the polls in Charlestown yesterday afternoon, voter Joanne Brew said she opted to vote for just three at-large candidates: Arroyo, Connolly, and Pressley.
“They reflect the character of the city,’’ said Brew, a retiree, adding that she wanted a council that mirrored the demographics of the city. “Boston has a thriving immigrant population.’’Martine Powers of the Globe Staff and Globe correspondents Patrick R. Rosso and Sara Brown contributed to this report. Andrew Ryan can be reached at email@example.com Follow him on Twitter @globeandrewryan.