The election featured millions of citizens voting for the first time after Chile greatly expanded its electorate, although absenteeism was also high.
Fernandez, 41, defeated incumbent Mayor Pedro Sabat of the center-right National Renovation party in Nunoa, a district of the capital. A socialist and veterinarian by trade, she served on the local council in the district after growing up in Cuba, where her mother Beatriz lived in exile after President Allende died during Gen. Augusto Pinochet's 1973 coup.
The left's biggest victory was in central Santiago, where Carolina Toha defeated Pablo Zalaquett of the ultra-conservative Independent Democratic Union. Toha served as former President Michelle Bachelet's spokeswoman, and her father, Allende's vice president, died after being jailed and tortured.
Toha had sided with the students protesting for free, quality education in Chile, while Zalaquett ordered police to crack down on their demonstrations.
"I will be a mayor for all," Toha said in her victory speech. "Everyone will be listened to; no one will be excluded."
For many members of Chile's student protest movement, which burst onto the scene last year with a series of massive demonstrations, this was their first chance to vote.
The left also won in the capital's upper-class Providencia district, where community leader Josefina Errazuriz ended retired Col. Cristian Labbe's 16-year-hold on the mayor's office. Labbe led Pinochet's domestic intelligence agency during the dictatorship and has tried to bring Pinochet's disciples back from the political wilderness.
Center-right politicians held onto five other major cities, including Vina del Mar, Valparaiso, La Florida, Las Condes and San Bernardo, but they lost southern Concepcion, where the mayor was sharply criticized for her handling of the earthquake aftermath.
In all, Chileans decided 345 mayor's offices and 2,224 local council seats nationwide.
With more than 90 percent of the vote counted, the ruling right-wing alliance was winning 37 percent of the seats, while parties of the divided left were winning 43 percent overall.
Former President Ricardo Lagos called Sunday's election, the first since Chile added five million new voters to the rolls by automatically registering all adults, the end of an era.
By making voter registration automatic, Chile increased its electorate from 8.1 million to 13.4 million in the nation of 17 million. But with voting no longer mandatory, many stayed home, dismaying those who had hoped that so much social upheaval would lead to bigger changes.
The old electorate had moved increasingly to the right as ever-fewer Chileans bothered to register and vote. After Sebastian Pinera's 2009 presidential win ended 20 years of center-left rule, his center-right alliance agreed to expand the electorate only if the left agreed to make voting optional.
Some analysts say the left's concessions were a mistake, noting that wealthier people are more likely to vote even when it's not mandatory. On Sunday night, the turnout appeared to confirm the left's worst fears: in some districts, absenteeism reached 80 percent.
Pinera called the absenteeism "a warning sign" for Chile's democracy and pledged that his government will do all it can to increase participation in next November's presidential elections.