The 22-year-old, nicknamed "chicharito" or "little pea", struck in the 85th minute of the Champions League Group C clash at the Mestalla shortly after coming off the bench.
"When he takes his chances it's like shelling peas, with either foot," the 68-year-old told a news conference.
The presence of Wayne Rooney, absent due to injury on Wednesday, and the in-form Dimitar Berbatov in the squad has limited Hernandez's appearances.
"He's young, he knows that," Ferguson added. "He's developing a lot in his game and getting some good strength work in the gymnasium. He still has some work to do on that aspect."
"You can't get away from the fact that he's a fantastic finisher and he showed that tonight," Ferguson said.
Hernandez's father, also called Javier, is a former Mexico striker who played at the 1986 World Cup and was known as "chicharo" (pea) because of his green eyes.
