In November 1864, the War of the Triple Alliance broke out, for which Duarte was summoned and assigned a group of men to be trained by him.

On April 27, 1865, a large column of the Paraguayan Army made up of about 10,000 men began their march towards Rio Grande do Sul, passing through the modern-day Argentine provinces of Misiones and Corrientes.

Duarte remained in command of the second group that was made up of about 3,200 men who advanced through Argentine territory until they reached the banks of the Yatay stream near Paso de los libres.

In this battle, the Paraguayans repulsed the initial attacks but due to numerical inferiority, they couldn't hold their positions for long.

The "Escuela Nacional General Pedro Duarte N°2525" at the District of Carlos Antonio López, Itapúa is named after him.