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."
Hernandez joined United in July from hometown club Chivas de Guadalajara, for whom he had scored 29 goals in 79 games after making his debut as a teenager in 2006.
His pace and skill helped him score twice for Mexico at the World Cup in South Africa shortly before completing his move to the Premier League.
"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.
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