With nearly all the votes counted, Macri took 51.5 percent of the runoff vote, just ahead of ruling party candidate Scioli on 48.5 percent.
"This is the beginning of a new era that has to carry us toward the opportunities we need to grow and progress," a dancing Macri told supporters at his headquarters late on Sunday.
"This is a historic day, a change of era which is going to be marvelous," Macri said.
Macri stood on a political platform to introduce liberal policies in a bid to boost Argentina's sluggish economy.
"By popular will, a new president has been elected: Mauricio Macri," leftist contender Scioli told supporters after 69 percent of the country's votes were counted.
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Welfare state vs. neo-liberalism clash in Argentine vote
Argentina's voters have a choice between contrary visions of their country in a historic election runoff that pits 12 years of a robust welfare state against neoliberalism. Irene Caselli reports from Buenos Aires.
Sunday's runoff followed elections on October 25, which witnessed Macri come in second to populist Peronist movement candidate Scioli. The two-time mayor of the Argentine capital only came to the fore in the election in recent weeks.
The polls showed Argentines opted for a political shift following 12 years of leftist rule under President Cristina Fernandez de Kirchner, and her late husband, who ruled before her.
"We made an effort and had the will to convince. I am a democrat and I respect the popular will, which has chosen an alternative," Scioli added.
Change of style
"Scioli did not manage to differentiate himself from Fernandez and so people stopped seeing him as a change of style and went over to Macri," said Mariel Fornoni, a consultancy firm director and political analyst.
Meanwhile, outgoing President Fernandez did not indicate whether she would continue to lead her party if Scioli lost at the polls.
"I am an activist. I have never seen myself as a leader in anything, I never order anyone anything, so don't get me into a debate that is not fit for a day like this," Fernandez said after casting her ballot.
"The future will be whatever Argentinians decide. Nothing lasts forever," Fernandez added.
Macri is expected to take office on December 10.
ls/jm (Reuters, AFP, AP, dpa)