Obama became the first US president to pay homage to the victims of the 1976-1983 military regime, which declassified documents have revealed was supported by top US officials.
He visited the Memory Park on the banks of the River Plate, a monument to the estimated 30,000 people who were killed or went missing under the dictatorship.
Alongside Argentina's President Mauricio Macri, Obama tossed white roses into the river in memory of those who were executed by the regime by being hurled from airplanes into the water in so-called "death flights."
"We cannot forget the past."
He alluded to the US role in the dirty war, saying each country "has to examine its own policies" and instances when "we have been slow to speak out for human rights."
Obama's two-day visit coincides with the 40th anniversary of a right-wing military coup, which the US government condoned and which ushered in the dictatorship.
Victims' groups had been angered by the choice of the date for Obama's visit, given the US support for the coup at the time.
The memorial in the park has a wall bearing the names of 20,000 victims and a further 10,000 empty plaques for others who have yet to be identified.
A jetty runs into the nearby river, commemorating victims of the "death flights.
