In a rare rebuke by a city electorate fond of its incumbent pols, voters on Tuesday replaced at-large city councillor Felix Arroyo of Jamaica Plain with West Roxbury's John Connolly, an attorney and former teacher who finished fourth overall. Incumbents Michael Flaherty, Steve Murphy and Sam Yoon - in that order - took the top three spots in citywide balloting. Yoon, who lives near Field's Corner, won the majority of Dorchester's precincts and made strong inroads citywide, replacing Arroyo as the leading minority vote-getter in Boston.

Voters awoke to a drizzly rain Tuesday morning, and judging by the turnout at the polls, many rolled over and went back to sleep. It was the lowest voting turnout in decades with just under 14 percent of registered voters dropping a ballot.

Nevertheless, for those paying attention, it was an exciting race in the final hours. Things got ugly. Tensions brewing between John Connolly and incumbent Stephen Murphy erupted into a flurry of negative mailings. Connolly started the mini-melee with two anonymous pieces accusing Murphy of repeatedly job-hunting while in the Council office.

Murphy then retaliated, calling Connolly a coward for not signing his accusations. The mainstream media finally woke up to both campaigns, and slammed Connolly for his mistake.

"Our back was right up against the wall," said the candidate's father, Michael Connolly, a former Secretary of State. "After a long flawless campaign, he made a mistake. But it was a very human mistake, and he admitted to it. This fight between Murphy and Connolly had been coming for months."

But in the endgame, it was Arroyo who lacked the votes to win the final at-large seat on the council. Connolly edged Arroyo out by, unofficially, almost 3,500 votes.

Progressive candidates traditionally lose out when turnout is low, and some are citing apathy among minority voters and a step back for the "New Boston." But incumbent and Team Unity member Sam Yoon ran strong across the city, narrowly missing the number two spot won by Murphy by under 500 votes. There may be more to it.

Compared to earlier years, there were fewer viable candidates on the ballot, organizing had a stronger focus in neighborhoods like West Roxbury, Dorchester and Hyde Park, and Boston's pols had fewer endorsement choices to make, as did donors.

"Last time around our allegiance was split," said Peter Sasso, a Connolly supporter from Melville Park. "There's only so much energy we can give each person."

In 2005, Sasso worked on Matt O'Malley's campaign. This year O'Malley threw his support and his volunteers to Connolly early. His father George O'Malley reportedly shook hands outside Florian Hall all day, and Connolly won that double precinct, even besting the city's ticket-topper, Michael Flaherty.

Connolly's strongest showing was his native Ward 20 in West Roxbury, where he pulled nearly a third of the vote with a relatively high turnout.

"Two years ago it was different," said West Roxbury's district Councillor John Tobin. "O' Malley and Patricia White were good friends of mine. This time it's clear, because John was the only one from the neighborhood that was running."

Arroyo's campaign, never strong on the fundraising front, depended heavily on Team Unity members and Yoon's campaign for a boost, according to Arroyo's campaign manager Rob Laurent. Yoon and Arroyo's numbers reflected each other in some predominantly African-American, Latino, and Asian precincts, but Arroyo didn't keep up in Wards 14 and 15 in Dorchester, Yoon's base, and other areas. The election's small field of candidates may have hurt Arroyo as well.

"We saw a huge surge of supporters in the last few days, but that's something we'd have seen much earlier if there had been a preliminary," said Laurent.

The state cancelled the preliminary election this year, at the recommendation of the City Council, because only nine candidates were on the ballot. The September preliminary would have narrowed the field to eight.

Arroyo was smiling, but perhaps a little wistful, at a Team Unity party at Slade's Bar and Grill in Lower Roxbury Tuesday.

"I'm feeling good," he said. "I'm feeling like mission accomplished. I did what felt like I should do for the people of Boston. People have a say and they determined that it is time for new people and I'm fine with that. I took risks that a lot of people would not have taken, but I would not have done it any other way."

Arroyo didn't speculate on his next move, but said he will continue to work on bringing progressive voices to Boston's government.

State Rep. Gloria Fox was less reticent about Arroyo's fall.

"Black, Latino and Asian voters have to remain together," said Fox heading towards her van after the Slade's event. "It still boils down to the communities of color against the non-community of color. I don't consider this a New Boston vote, this was a back to the same vote. Anyways, Connolly got some help."

At least some of Connolly's help came from communities of color. Suffolk County Sheriff Andrea Cabral and state Sen. Dianne Wilkerson endorsed Connolly.

"My support grew in communities of color, but particularly in African-American communities where I think the fact that I am a lifelong resident of Boston and a teacher resonated," said Connolly. DISTRICT INCUMBENTS CRUISE TO RE-ELECTION In three races for district City Council seats, Dorchester's incumbents held strong. Carlos Henriquez won 18 percent of the vote in District 7, leaving incumbent Chuck Turner supreme with 81 percent. In District 3, Council President Maureen Feeney won handily over Michael Coté with 82 percent of the electorate. And in District 4, Councillor Charles Yancey took 89 percent, leaving a mere 10 percent to J.R. Rucker.

"We never take any race for granted," said Yancey at a Team Unity celebration at Slade's Bar and Grill in Roxbury. "We were working hard as if we were up against someone with $2 million in the bank."