The Manchester United forward was made a doubt for Saturday’s opening Group D game against Italy in Manaus after limping out of training on Tuesday.
Welbeck, 23, took part in the early part of Tuesday's session in Rio de Janeiro with strapping over his thigh but was withdrawn, and he became one of two current absentees on Wednesday along with Alex Oxlade-Chamberlain.
The Football Association's refusal to comment on the severity of Welbeck's injury set off alarms bells, but Rooney has moved to allay those fears when he spoke to the media after the session.
"Danny will be fine,'' he said. "I am sure he will be ready for Saturday.
"He's just not risked anything in training today, so he'll train on Friday and he'll be available for Saturday I'm sure."
Arsenal’s Chamberlain is currently recovering from the knee ligament injury he sustained against Ecuador and faces a battle to be fit for England’s second group clash against Uruguay.
If Welbeck is ruled out, the chances of Raheem Sterling starting the match will be vastly increased.
Manager Roy Hodgson has resisted the temptation to shower praise on Ross Barkley and Wayne Rooney since the England squad met, but that has not been the case with Sterling.
Sterling missed England's final warm-up game against Honduras in Miami after he was sent off in a brief substitute appearance against Ecuador at Sun Life Stadium.
Sterling did not start England's final home game of the season against Peru, meaning he has only had 39 minutes' worth of action since the squad got together on May 19.
He appears to be in pole position to start the Italy game, though - either as a winger or in the number 10 position just behind Daniel Sturridge.
"If I select him, it won't be a risk that he hasn't played so many minutes," Hodgson said.
"He's as fit as a flea and I'm pretty certain he hasn't forgotten how to play matches, either.
"It was unfortunate that he couldn't play the (Honduras) game (because of suspension), but I can tell you that Raheem Sterling is very much in the group of players I'm considering."
Hodgson, meanwhile, confirmed his squad had taken their anti-malaria tablets on Tuesday morning despite concerns over the side-effects.
Generally, one in 10 people experience stomach cramps, sickness or dizziness after taking the pills.
The last thing Hodgson wants is to lose one of his players to illness, but the England manager has been left with no option but to issue the anti-malarials to his players.
He said: "As far as I'm concerned, I've got to go with medical opinion and if the doctors are telling me that when we go to Manaus, the players must take malaria tablets, whether it has side-effects or not, what do I do?
"I can't turn around and say 'We will not take malaria tablets', because the bottom line is better stomach cramps or whatever it is for one player in 10 than have someone contract malaria because that would be unthinkable."
Interestingly, Hodgson did not take any anti-malaria drugs before a trip to Manaus last year, but the FA confirmed he has done so this time around.
"I went to Manaus and I didn't take any for the two days I spent there," Hodgson said.
"That might just be something to do with the fact that I'm not a football player."
After consulting FIFA's chief medical officer Professor Dr Jiri Dvorak, England have decided not to have their yellow fever vaccinations.