Police said the youth was 14 years old. Local media identified him as Manuel Gutierrez, and said he was shot near a security barricade as protesters battled police in Santiago on Thursday, the second day of a two-day strike against unpopular Pinera marked by violent clashes and sporadic looting.
Local radio said witnesses blamed police for firing the shots.
"The death of any citizen is a very serious situation," said Rodrigo Ubilla, undersecretary at the Interior Ministry. "We should all be sad today because we have not been able to move forward peacefully."
"The solutions to big problems in this country do not lie in throwing stones, bombs and attacking people, the solution lies in talking," he added. Ubilla had put the youth's age at 16.
Led by students demanding free education, hundreds of thousands of people have taken to the streets in recent months to call for greater distribution of the income of a copper price boom in the world's top producer of the metal.
On Thursday, youths blocked roads, threw rocks and set fire to piles of trash at intersections in Santiago and other cities to block traffic. Police used water cannon and tear gas to defuse the latest social unrest against conservative billionaire Pinera's policies.
The government said more than 1,300 people have been detained since Wednesday and several police officers were badly wounded -- two of them shot -- as violence flared when dozens of shops and supermarkets were looted and buses damaged.
Organizers said around 600,000 people joined Thursday's protest across Chile. Reuters reporters estimated crowds in the capital alone at around 200,000 people.
Operations at some of the world's biggest copper mines were not affected by the protests, which also seek to pressure the government into raising wages and revamping the constitution and tax system.
While Latin America's model economy is seen expanding 6.6 percent this year and is an investor magnet thanks to prudent fiscal and monetary policies, many ordinary Chileans feel they are not sharing in the economic miracle.
Investors, long used to economic stability, are weighing risk, although markets have taken the protests in stride.
Previous governments have faced one-day national strikes but this was the first 48-hour stoppage since the 1973-1990 Augusto Pinochet dictatorship. A recent poll showed Pinera as the least popular president since Pinochet's rule.
Even a major cabinet reshuffle last month, the second since Pinera took power in March 2010, has failed to quell unrest.
The unrest has been a lightning rod for wider protests from environmentalists to copper miners
Workers at some of the world's biggest copper mines have staged strikes of their own to demand a bigger share of windfall copper profits. Workers at BHP Billiton's Escondida, the world's No.1 copper mine, halted a two-week strike earlier this month that stoked global supply fears.