The England striker was initially ruled out for up to three weeks with an ankle injury, although the Red Devils boss later indicated United’s No.10 may be on the sidelines for a longer stretch.
Mexico international Hernandez has excelled in Rooney’s absence and has already scored three goals in his last two appearances for the Red Devils.
Coinciding with Rooney’s lengthy spell on the sidelines, the 25-year-old has suffered a dip in form and has failed to regain the momentum that saw him top the club's scoring charts last season.
Ferguson has been impressed with Hernandez’s form and insists the 22-year-old will not automatically be replaced once Rooney is back to full fitness.
"His [Hernandez's] performances have dictated that [the praise he has received]," Ferguson said, according to The Guardian.
"We had a feeling he would break through and, therefore, it gives you a [selection] problem, but the right kind of problem.
"It will be difficult [leaving Hernandez out]. I'm not even suggesting he will be left out. He's keeping his place in the team because he deserves to keep his place in the team."
United suffered a turbulent week during Rooney’s controversial transfer saga although Ferguson is adamant it is time to lay the issue to rest.
"It's all over, it's all left in the past," he added. "He's signed a five-year contract, we're happy and we kick on.
"There have been plenty of difficult issues at this club over the years. You could say this was a big one but only in the sense it was a top player.
"Plenty of players come to a situation with their contracts. The difference is that they are normally done very quietly and unnoticed.
"But every club has these problems, once the players get to that two-year line when you have to start thinking about how to deal with it.
"All these issues are there for everyone these days. It's just much more difficult than it was even three years ago."