In front of a loud and overwhelmingly Mexican crowd of more than 70,000, 'El Tri' were unable to put away their chances in the regulation 90 minutes but made amends during extra-time.
"It was tough, Honduras were very well organised, strong and we couldn't find much space," Mexico head coach Jose Manuel de la Torre told reporters.
"We should have finished it off in regulation but it didn't work out that way."
Honduras went close themselves to a late winner inside the 90 minutes but Mexico took control in extra-time, producing the clinical finishing that makes the difference.
De Nigris produced a superb header to put Mexico ahead in the third minute of extra-time, rising to meet a corner from Pablo Barrera.
Manchester United forward Hernandez then pounced from close range after another De Nigris header from a corner was pushed out by Honduras keeper Noel Valladares.
The goal was the seventh in five games in the tournament for Hernandez, who is also known as "Chicharito" (little pea) and has become a national hero in his homeland.
Honduras had Roger Espinoza sent off for a second yellow card with five minutes of extra-time remaining.
Espinoza had earlier gone the closest to producing an upset when he unleashed a fierce drive in the 90th minute from 25 metres, which forced Mexico keeper Alfredo Talavera into a fine save.
Before that, Mexico had their chances with Hernandez missing a golden opportunity with a header and more glaringly, Giovani dos Santos dragging a shot wide after being put through clear on goal.
In the end though, it was the extra sharpness from Mexico in the additional period that made the difference.
"It was like a final, we had to be really focused physically and mentally. The attentiveness we showed in the 90 minutes just wasn't there in extra-time," Honduras coach Luis Fernando Suarez said.
Saturday's clash at the Rose Bowl in Pasadena will be the third consecutive Gold Cup final featuring the United States and Mexico.
While the Americans got their semi-final against Panama resolved inside normal-time, the Mexicans will have to recover from an extra 30 minutes.
De la Torre, however, said that the extra exertion should not count against them in California.
"The team has done well in regeneration... they are tired but are well prepared. We will just have to see how they recover from any knocks picked up," he said.
