Hernandez's 85th-minute strike proved the difference as United beat Valencia 1-0 in a keenly contested Champions League encounter at the Mestalla. The result leaves Ferguson's side well placed in Group C heading into their back-to-back games with unfancied Bursaspor.
United appeared happy to settle for a point in their second group game, but the late introduction of Hernandez and Federico Macheda turned the match in the visitors' favour, according to Ferguson.
"I think the second half we improved, had more penetration about us, but when you come here you have to make sure you're solid at the back,'' Ferguson told ITV1. "I don't think they made any really great chances, but they're always a threat because they play good football. I think what Chico did was he brought in penetration.
"There was a moment before he scored his goal where made a great run in behind them, and that's what we needed at that stage of the game. The changes suited us in terms of giving us energy and speed. It's a great result for us. It's not easy coming here. We're pleased to win.''
For Hernandez, it was a goal to savour.
"The goal will give me so much confidence,'' he said. "I am only at the start of my career with United and to score so early in the Champions League is a big boost. I always used to watch the Champions League when I was back home in Mexico.
"It is one of the most important tournaments in the world, so I was always keeping up with it. It is great to be a Manchester United player and I want that to continue for a long time.''
And Ferguson explained that Dimitar Berbatov's impressive recent displays are to balme for the Mexico World Cup star not featuring much since his debut goal in the Community Shield.
"The form of Berbatov has delayed his appearances,'' Ferguson said. "Of course, Wayne Rooney and Dimitar were the natural choices at the start of the season, which has meant Javier has not had a lot of football.
"But he is young and he is developing his game and doing good work in the gymnasium. He still has work to do in that aspect of his physique but you cannot take away from the fact that he is a fantastic finisher.
"The way he took his chance, it was like shelling peas. It was so natural to him.''
Although he broke his English duck in bizarre fashion in the Community Shield, to get his first competitive goal offers Hernandez a chance to build his United career free from pressure.
"It was a great night,'' Hernandez said. "I am so happy about the goal but also it was important to get the win and the three points. I always used to watch the Champions League when I was back home in Mexico. It is one of the most important tournaments in the world, so I was always keeping up with it.
"The goal will give me so much confidence. I am only at the start of my career with United and to score so early in the Champions League is a big boost. It is great to be a Manchester United player and I want that to continue for a long time.''
Hernandez's late effort settled a game of few chances. Although Valencia had plenty of possession, they were rarely able to break through the United rearguard and Edwin van der Sar made only one save of note.
Rio Ferdinand partnered Nemanja Vidic in central defence for the first time this season as United's back four took on a more familiar look.
Ferdinand is still nursing his long-standing back complaint, to the extent that he stood up for most of the flight to Spain on Tuesday, but was given his chance by Ferguson, who was happy to see his defender return.
"Rio needed a game like that, Ferguson said. "He has the experience, which was vital and the ability to keep the ball, which is important. His experienced helped us. There is no question about that. For his first real game in a long time we are very pleased with that.''
Ferdinand himself admitted that he was delighted with his first real test since coming back from injury.
"It was good. I'm just pleased to be back and playing - it's what I know and what I do best,'' Ferdinand told ITV. "To get out there and play 90 minutes was fantastic. To get a win in Spain is hard and we've done it today.
"It's definitely a confidence-booster. It's been well documented that we've let points slip in recent games and you do get nervous on a run like that, but today I thought as a team we dealt with it well.''
Ferdinand also reserved praise for matchwinner Hernandez, saying: "He's a fantastic lad. He comes in early for training every day and he's one of the last to leave. He's got a great attitude, wants to learn, wants to get in the team. But that's the same for all the lads.''
The victory, only United's second in 19 games against Spanish opposition on Spanish soil, is a blow to Valencia, who hammered Bursaspor in their opening game and now must tackle back-to-back confrontations with Scottish champions Rangers.
"They will be two physical games,'' Valencia coach Unai Emery said."Both matches are going to be very important to us.
"However, we are also looking forward to playing Manchester United again at Old Trafford, when we will have to be at our very best. We are disappointed with the result tonight but I am quite happy with the way we played.''