According to partial results, this comes after former communists swept to victory in the first round.
There are several hundred political parties in Bulgaria, with most of the larger parties being composites of smaller parties.
Sofia Mayor Stefan Sofiyanski, who was backed by the opposition Union for Democratic Force (UDF) party and Prime Minister Simeon Saxe-Coburg's centre-right National Simeon II movement party, secured re-election in the capital.
The UDF is a coalition of several parties, including the Bulgarian Agraraian People's Union and the Bulgarian Social Democratic Party.
In Plovdiv, Bulgaria’s second-largest city, Mayor Ivan Chomakov took 52% of the vote, according to Gallup, MBMD and three other polling institute projections.
“Democracy has resisted attempts to restore communism,” Nadedzha Mikhailova, president of the UDF told reporters after the second and final round of voting on Sunday.
Mayoral nominees were being decided in 1532 cities and villages across the southern European country in a mid-term vote in advance of legislative elections due in 2005.
The high level of abstentions – turnout barely reached 39% -indicated Bulgarians' disenchantment with the political process in general.
The elections come 800 days after Saxe-Coburg, who returned in 2001, was swept to power on pledges of improved living conditions. Bulgarians are frustrated by high crime rates and poverty.
Saxe-Coburg was a boy king before seeking exile in 1956 when the communists took over the country.
Sofiyanski took 53.6% of the vote in winning a third term, against 46.7% for the former communists' candidate Stoyan Alexandrov, according to official results with 76% of ballots counted.
The former communists in the Bulgarian Socialist Party (BSP) were less overwhelming in the second round than they were in the first on 26 October, when they won four of the six major cities.
The BSP took 33% of the first round vote. The UDF was next with 21% while the prime minister's party polled only 10%, as did his coalition partner the Turkish minority Movement for Rights and Freedoms party.
“The largest party in Bulgaria is made up of the people who do not vote,” analyst Petar Emil Mitev told AFP.
Bulgaria has a sizeable Muslim community, making up 13% of the total population and comprised of mostly Turks. In the 1980s, leader of the Movement for Rights and Freedoms, Ahmad Dogan, played a role in defending Turkish minority rights.
In the 1997 election though, Dogan opted for a coalition with larger parties in the Union for National Salvation.