Rooney's hamstring injury and Hernandez's dead leg have ruled the potent striking duo out of the Group C match at Old Trafford, paving the way for the likes of Dimitar Berbatov, Michael Owen and Danny Welbeck to make their mark.
Even if they had not been injured, Ferguson may well have looked to his back-up players - which include last season's joint top scorer in the league and England's fourth highest international scorer.
"Having a squad gives them a better chance of winning things, so they've accepted [the squad system] a long time ago," Ferguson told a news conference on Monday.
"And they want to do well when they get the opportunity because as a group we all want to do well.
"They all have a part to play in the context of the number of games you have in the Premier League, Champions League, League Cup, FA Cup, it's an exhausting season unless you use your squad."
Berbatov, who scored 20 goals to share last season's Premier League golden boot, found himself edged in the second half of last term as Hernandez's goal-poaching prowess was preferred to the Bulgarian's more languid approach.
Owen showed last week the devastating touch that netted him 40 England goals in 89 internationals was still there with two goals against Leeds United in the League Cup.
Both would be glad to be given a chance to shine at Old Trafford on Tuesday in Europe's elite club competition but face competition from youngster Welbeck, who was given the nod ahead of them when Hernandez was sidelined earlier this season.
ON YOUR TOES
Winger Ashley Young, who missed United's 1-1 draw at Benfica in their opening Group C game earlier this month, is hopeful of making his first Champions League appearance against Basel but is aware there is no guarantee.
"When you come to a club like Manchester United, you are going to be challenged," the 26-year-old, who joined United from Aston Villa in the close season, told the news conference.
"It's always nice to know you've got to be on your toes 24/7 in training every day, you've got to go out there and give 100 percent because you know someone else could take your spot."
The attacking berths are not the only ones up for grabs as injuries to Chris Smalling [groin] and Jonny Evans [ankle] have created vacancies in defence.
Captain Nemanja Vidic remains sidelined with a calf problem and Ferguson hopes the centre-back might have recovered from it by the time the two-week international break is over in the middle of next month.
The manager had no idea when Rooney, who has already scored nine league goals this season, would return but said Hernandez should be available for Saturday's league game against Norwich City.
Without Rooney and Hernandez, who missed most of Saturday's league game at Stoke City after being forced off early, United dropped their first points of the season with a 1-1 draw although they still top the Premier League on goal difference
