It was the seventh win in 11 games for Mexico at the confederation finals, with its four losses coming against its North American neighbors.
The loss was the first in a competitive match in the 2012 cycle for Trinidad, which won all seven of its Caribbean qualifiers by a combined 58-0.
Hernandez, from Corona, California, gave Mexico the lead in the 32nd, and Duarte, from Tucson, Arizona, doubled it in the 39th, enabling it to match the United States on points in Group B. The Americans routed the Bahamas 10-0 in the first match of Thursday's doubleheader.
Mexico controlled much of the game, generating its first corner in the second minute and allowing only sporadic possession and occasional chances by Trinidad.
After only a handful of genuinely dangerous moments, Mexico went ahead when Hernandez - one of 11 U.S.-based players on the Mexican roster - settled a cross from Taylor Alvarado on the right side of the area, took a touch and arced a left-footed shot over the outstretch arm of Trinidad keeper Lebrisca Phillip.
Trinidad had its most dangerous moment two minutes later when Donika Murray found some space on the right side and unleashed a right-footed drive from the edge of the penalty area that Mexican keeper Gabriela Paz had to punch over the bar.
Alvarado, another of the U.S.-based players from Santa Paula, California, set up Duarte for the second as well.
She raced around Trinidad defender Shanisa Camejo on the right side and sent in a cross to Duate, who beat Diarra Simmons to the ball and one-timed a right-footed effort from 10 meters inside the right post.
Mexico continued to control the game in the second half, restricting Trinidad's opportunities to chances from distance.
Trinidad lost Canejo to an apparent leg injury in the 75th minute, and her long-term prognosis was unknown.
Mexico will next play the Bahamas on Saturday while Trinidad will face the United States.