The trio will be on the sidelines as Sir Alex Ferguson decides not to risk them for the Red Devils in Sunday's showpiece derby against their arch-rivals at Wembley
Mexican striker Hernandez was a revelation in his debut season at Old Trafford last year but is being handled carefully following a concussion suffered in pre-season.
Manager Sir Alex Ferguson said at his pre-match press conference: “Hernandez is still two to three weeks away.
“He should be back at the end of August.
“Considering he had a concussion some years ago, we're playing it safe.”
England midfielder Carrick complained of “feeling a tightness in his Achilles” during Wednesday’s testimonial game for recently retired goalkeeper Edwin van der Sar and will be kept out of the Community Shield as a precaution.
Full-back Rafael picked up a knock in the friendly victory over Barcelona last week.
Darren Fletcher and Antonio Valencia have, however, returned to training, although neither is likely to appear on Sunday.
“It's very easy to get emotional about this type of game,” Sir Alex said on the subject of the upcoming derby match.
“I don't think we'll be changing our policy.
“I've always viewed the Community Shield as a stepping stone for the first game of the season and there are two or three players who will need a game.”
United are the current holders of the Shield, having beaten Chelsea last year.