The pair were notable absentees as United prepared for their upcoming Group C clash with defenders Nemanja Vidic (calf), Chris Smalling (groin) and Jonny Evans (ankle) also missing the training session at Carrington.
Training day: Dimitar Berbatov and Michael Owen look set to lead the line against Basel at Old Trafford
Mexican striker Hernandez was an early casualty in Saturday's 1-1 Barclays Premier League draw at Stoke when he was forced off following a collision with goalkeeper Asmir Begovic and defender Jonathan Woodgate.
Missing man: Javier Hernandez was carried off after three minutes against Stoke
Rooney, however, was missing altogether with a hamstring problem and manager Sir Alex Ferguson is unlikely to be able to call upon him before the international break next week making him a doubt for England's crunch Euro 2012 qualifier against Montenegro on October 7.
Talking tactics: Sir Alex Ferguson speaks to assistant Mike Phelan and club legend Bryan Robson at the club's Carrington training complex
Ferguson confirmed on Monday that Rooney would miss the match with a hamstring injury and said that it was difficult to know when the Englandstriker would be back in action.
Ferguson told a news conference at Old Trafford: 'He's not playing tomorrow. It's difficult to assess with hamstrings but we hope we have him back quickly. He did a bit of joggingthis morning but that's all.'
Ferguson also said that Hernandez's dead leg would keep him out but thatthe Mexican should be back for the home match against Norwich on Saturday.
Injury doubt: in-form Wayne Rooney has a hamstring complaint and did not train on Monday morning
Dimitar Berbatov was selected alongside Hernandez for what was only the Bulgarian frontman's first start of the season.
Fresh from his Carling Cup heroics against Leeds last week, Michael Owen replaced Hernandez but will be competing with fit-again Danny Welbeck for a place in the starting XI.
First start: Dimitar Berbatov has failed to register a goal so far this season
Michael Carrick, who was not in squad for the visit to Stoke, returned to training and will hoping to find a way back into United's European plans.
On the ball: Darren Fletcher keeps possession as Rio Ferdinand and Park Ji-sung look on
Ferguson, who was joined by United legend Bryan Robson at the club's training ground on Tuesday, admitted he is keen to rotate his squad against the Swiss champions.
'Maybe I'll use some of them against Basel,' he told the club's official website.
In the frame: Owen is hoping to extend his recent stay in the first team with a run-out against the Swiss champions
'I do need to get all the squad moving. I think there will be changes on Tuesday.'
'Basel are a decent side though. Thorsten Fink [the manager] was a substitute in the final for Bayern Munich in 1999 when he came on for Lothar Matthaus. I spoke to him at the UEFA conference and he's done a good job.
'If you get to 10 points, you know you're into the next stage but we'd like to win the group anyway. If we win our next three games, we can utilise the squad. It would definitely help and we've done that over the years.
Fit again: Danny Welbeck, training with Ashley Young, has returned from a short lay-off and hoping to reclaim his starting berth in the side
Ferguson, however, is mindful of previous slip-ups in the competition after making wholesale changes but insisted whoever makes his starting team will be good enough to win the game.
'It's sometimes backfired,' he added. 'I played a fresh team over in Fenerbahce and they beat us 3-0.
Euro star: David de Gea trains ahead of Tuesday's Champions League clash
'Although I want to make changes, I don't want an embarrassment. So changes have got to be made with a mind of still winning the game.'
Last season's finalists United drew their opening Champions league match with Benfica in Lisbon a fortnight ago, while Basle are group leaders after defeating Romanian side Otelul Galati in their first game.
Defiant De Gea passes Stoke's physical examination at The BritanniaRooney scare for England after injured striker ruled out of next two United gamesChampions League digest: Cole finds his feat with Lille beautyMan City to put hostilities aside to lay wreath commemorating Munich Air Disaster ahead of Bayern matchAll the latest Manchester United news, features and opinion