Fernandez had earlier declined an invitation from Brazil's President Dilma Rousseff to attend the final, saying she was recovering from a sore throat. Her counterpart, German Chancellor Angela Merkel, attended the match, even leaping with joy at Germany's winning goal.
In a televised speech, Fernandez, flanked by Lionel Messi and the rest of the team, said: "As you know I'm no soccer fan."
"I didn't see a single match, not even the one yesterday," she said, adding that she rang Argentine Coach Alejandro Sabella after the match because it felt like the team had won.
"That's how I felt and how 40 million Argentines felt too."
Although not entirely surprising given her well-known disinterest in the sport, Fernandez's comments will do little to endear herself to a country obsessed by soccer and left heartbroken by the defeat.
Despite her best intentions, analysts said Fernandez, who cannot run in next year's election, failed to capture the national mood.
"It sort of underscores that she lives in a world of her own more and more," said Felipe Noguera, a political analyst.
"This has been a very positive month for the country and for the overall mood. And she's just not part of it," he added.
The team's run to the tournament final handed Argentina's 40 million people a rare chance to wipe from their minds the country's latest debt crisis, surging prices and political scandals.
Some fans took to social media site Twitter to vent their derision toward Fernandez.
"There is poverty, she doesn't see it. There is insecurity, she doesn't see it. Argentina's in the final, she doesn't see it. CFK blind woman," said one Twitter user, using the president's initials.
The players had been expected to head to Buenos Aires' iconic Obelisk monument in the afternoon to greet fans who partied there until late last night, celebrating their team's performance with dancing, drummers and firecrackers.
The festivities turned sour when dozens of hooligans hurled bricks and bottles as riot police replied with tear gas and water canons.
More than a dozen police officers were injured and 120 people detained, local media said.
Argentina's soccer federation said Monday's homecoming party had been canceled due to transport concerns.