The second-round vote will be held on January 17, with the winner succeeding Michelle Bachelet, the incumbent leftist leader, who is constitutionally barred from seeking re-election.
Pinera's victory would mark a shift to the right in a region dominated by leftist leaders but he is not expected to overhaul economic policies that have made Chile a model of stability.
Should Pinera, 60, win the second round vote, it would pave the way for the first right-wing government installed in Chile since General Augusto Pinochet's 1973-1990 dictatorship.
"We have to understand that this win doesn't belong to us," Pinera said in a victory speech to his party members.
"Eduardo Frei and Sebastian Pinera are too much alike ... They don't represent hope, nor change, nor the future"
Marco Enriquz-Ominami, a left-wing independent candidate for the Chilean presidency
"It belongs to all Chileans, to the humble people, to the poor and the middle class, the people who most need change from their government."
Frei, 67, who governed Chile from 1994 to 2000, urged leftists to unite in order to defeat Pinera in the runoff.
He pledged to adopt some of his left-wing rivals' ideas, and promised to give women and young people a prominent place in his government.
"The people have told us that there are things they don't like, that things must change, and I share this mission," said Frei, 67.
The support for Frei of Ominami, a former film-maker who ran as an independent, in the runoff vote could be the decisive factor in who wins the presidency.
Ominami has so far refused to endorse either Frei or Pinera for the poll, saying that "Eduardo Frei and Sebastian Pinera are too much alike".
"They don't represent hope, nor change, nor the future," he said in his concession speech on Sunday.
The leftist coalition that has run the country since Pinochet stepped down in 1990 has been credited with developing the region's highest standard of living, but it has been weakened in recent years by infighting and defections.
Many voters feel the ruling left has not done enough to redistribute Chile's wealth [EPA]
A huge wealth gap between rich and poor and a chronically underfunded education system also have many voters feeling more must be done to redistribute Chile's copper wealth.
A World Bank study several years ago showed that the poorest 10 per cent of Chileans benefit from only 1.3 per cent of government revenues, while the richest 10 per cent benefit from 40 per cent.
Lucia Newman, Al Jazeera's editor for Latin America reporting from the Chilean capital Santiago, said next month's runoff was likely to be a very tight race with big spending by the two leading candidates.
Both men had already put out their new slogans for the second round of voting even before the release of the final tally in the first round.
Our correspondent said there were two arguments to what appears to be a major swing from political left to right in Chile.
"One is that it's better to let things get worse before they get better, and clean the house within the coalition parties - even if that means having to live with a conservative government for one or two political terms.
"The other is that it is a very dangerous proposition. Once you let the right-wing in, it's very hard to get them out again, and that its better to transform the coalition from within - something that hasn't really happened over the last 20 years."