Electoral authorities said the 68-year-old conservative, who previously led the South American nation from 2010-2014, had 55 percent of the vote, with 98 per cent of ballots counted.
His leftist rival Alejandro Guillier, a 64-year-old TV presenter turned senator who ran as an independent backed by outgoing center-left President Michelle Bachelet, conceded after receiving 45 percent.
"We have suffered a tough defeat," Guillier said. He called for the opposition to "defend" reforms started under Bachelet.
He said Pinera walked away with "a solid and impeccable triumph."
He will once again take over from Bachelet, who was barred by the constitution from running for re-election.
Bachelet and Pinera have tag-teamed the presidency since Bachelet first took office in 2006. Since then, they have alternated in power, switching Chile's politics between center-left and center-right each time.
Pinera supporters were gathered outside his election headquarters in anticipation of his victory speech.
The outcome of the runoff had been far from certain after Pinera scored a much lower than expected 37 percent in the first round of the election held November 19.
But in the end, most voters appeared to come down in favor of the experience of Pinera, who is worth some $2.7 billion and painted himself as a safe pair of hands for Latin America's fifth-biggest economy.
Voting had taken place under a somber cloud Sunday, following the deaths of five people and the disappearance of 18 more in a mudslide in the country's south.
Both candidates had projected confidence, with Pinera stating as he cast his ballot: "I have the firm conviction that we are going to win these elections and that better times are going to come for all Chilean households."
Marco Moreno, of Central University, had called it "the most uncertain election since the return of democracy" after the end of Augusto Pinochet's dictatorship in 1990.
Although copper exports, which contribute greatly to Chile's wealth, are increasing thanks to demand from China and from the burgeoning manufacture of electric cars, the country is struggling relative to previous years.
Its GDP is forecast to expand a modest 1.4 percent this year, the slowest pace in eight years. Forecasts suggest it will grow 2.8 per cent next year.
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