Pinera, a conservative billionaire who holds a 26 per cent stake in LAN, resisted pressure to divest holdings ahead of Sunday's election.
His stake is now worth more than $1.5bn.
The windfall has angered Chile's leftwing-dominated media and outgoing government, which is still digesting its electoral defeat.
Andres Velasco, Chile's outgoing finance minister, said: "My opinion as a citizen is that, if the then-candidate [Pinera] had sold his shares at the right time - before and not after the election - that would have been much more preferable."
Michelle Bachelet, the outgoing president, who was constitutionally barred from seeking re-election, had raised conflict-of-interest questions over Pinera's LAN stake during the presidential campaign.
Pinera, who also owns one of the country's four television networks and the popular Colo-Colo football club, set up a blind trust to manage about $500m of his fortune, and promised specifically to sell his LAN investment if he won the election.
On Wednesday, he reaffirmed that pledge, saying "I will fulfil that commitment."
He said: "I am already very disconnected [from the investments]. The truth is that I have not been following the stock market over the past few days."
Fernando Barros, the president of Axxion de Pinera, the investment company that controls most of Pinera's LAN shares, said the president-elect is following through on campaign commitments to sell investments to avoid conflicts as president.
Axxion called an extraordinary share-holders meeting for February 5 to decide the sale.
Once that is out of the way, Pinera, the first conservative candidate to be elected in Chile in 20 years, has another potential conflict brewing with his plans to possibly privatise part of Chile's copper-mining giant Codelco.
Copper is Chile's most important export, and Codelco, the world's largest copper-mining firm, accounts for $31bn in annual revenues for the government.
Even though Pinera has not revealed his plans, economists believe he is looking at selling off 20 per cent of the company.