"It's not a drop, it's a collapse (in voter participation)," the leading Corriere della Sera daily said in an editorial. "This is disenchantment."
Rome's right-wing mayor Gianni Alemanno is facing a stiff challenge from centre-left challenger Ignazio Marino, who won nearly 43 percent in the first round compared with 30 percent for the incumbent, a former neo-fascist.
As of Sunday evening in the two-day polls, turnout stood at just under 34 percent, some 8.5 percentage points lower than in the first round two weeks ago, when turnout was already 15 points down on city polls in 2008.
Voting was to end at 1300 GMT, with results expected shortly afterwards.
Marcello De Vito, the candidate of the Five Star Movement of populist firebrand Beppe Grillo, did not back either candidate after scoring just 12 percent in the first round, but the party tends to sympathize with the left.
Independent candidate Alfio Marchini, who came last in the first round with 9.5 percent, also did not indicate his preference, although he has been openly critical of Alemanno.
Victory for Marino would be a shot in the arm for the centre-left Democratic Party (PD), which lost ground in this year's inconclusive general elections, while Silvio Berlusconi's centre-right People of Freedom Party (PDL) has fared poorly in previous recent municipal votes.
Analyst Antonio Noto of the IPR Marketing polling institute blamed the low turnout on the economic crisis.
"The numbers show that local administrators including mayors are losing sway because of the crisis. Lacking financial means, they cannot carry out repairs or improve services," he told the left-leaning daily La Repubblica.
But sociologist Piergiorgio Corbetta, writing in the Rome daily Le Messagero, sees the low turnout as an "alarm signal (that) politicians continue to ignore."
The Five Star Movement suffered a rout in the city polls after riding a wave of discontent with politics as usual to win 25 percent of the vote in the February general elections.
None of its candidates scored better than third place in the first-round vote in 563 towns and cities, so they were absent from the run-offs.
Analysts say Grillo's relentless attacks on Italy's governance have destabilized the movement. Last week the former comedian described parliament as a "smelly tomb, good for nothing".
Alemanno won Rome's mayoral election in 2008 on a strong anti-crime platform.