The mayor of Buenos Aires is one of the country's most powerful jobs and Kirchner had publicly involved himself in the contest in an attempt to broaden his political base before presidential elections in October.
The president had portrayed Macri as the second-coming of former president Carlos Menem, who was widely blamed for Argentina's economic crisis in 2001-2002.
Kirchner blamed the crisis on heavy borrowing and unchecked public spending during the Menem years and says Macri "represents the interests of the neo-liberal model".
He was alluding to Macri's family businesses that flourished in the Menem era, from the Boca Juniors to export ventures and a lucrative private postal service contract.
The mayor of Buenos Aires is one of the most
powerful positions in Argentinian politics [AFP]
Analysts say Macri's win could position him well for a 2011 presidential run and emerge as the leader of a fractured opposition struggling to gain ground on the highly popular incumbent in the race for the presidency.
"This affirms Macri as the figurehead of the opposition," Joaquin Morales Sola, a political columnist at the Buenos Aires daily La Nacion, said in televised comments.
But Macri has decided instead to focus on local issues such crumbling schools, budget overruns and garbage collection in appeals to the 2.5 million registered voters.
"Tell Kirchner ... I'm not a candidate for president," Macri said. "We aren't going to get into a debate about national political models."
The 48-year old benefited from his high-profile as the owner of the team where Diego Maradona once starred, whereas Filmus has a much lower profile.
He appeared before millions of television viewers on Wednesday as he saluted his team's victory in South America's premier football tournament, the Copa Libertadores.
Kirchner has dominated Argentinian politics since taking office in 2003, consolidating his power as citizens credit him with engineering the country's economic recovery.
Public opinion surveys show Kirchner and his wife, a senator, holding substantial leads in the presidential race, with either expected to win easily.
Neither has announced they are running but Kirchner frequently hints his wife may run in his place.