United's 100 per cent start to the Barclays Premier League season came to an end in Rooney's absence and the 25-year-old had earlier 'Tweeted' that he was 'gutted' he had been unable to play, but hoped he would be fit to feature in the Champions League clash with Basle at Old Trafford on Tuesday.
Injury blow: Rooney was 'gutted' to miss Stoke game
However, when asked about Rooney's condition after the match at the Britannia Stadium, Ferguson told MUTV: 'It is difficult to say. It's a hamstring. It is not a serious one, it is a mild one.
'I don't think he will be available for next week. It will be more than a week out.'
England are next in action in Montenegro on October 7, when a point is all that is required to reach Euro 2012, and national manager Fabio Capello will hope to have Rooney available.
With Ferguson having brought Dimitar Berbatov into his first XI to replace Rooney, the United manager then lost Jonny Evans to injury in the warm-up and had to call in Antonio Valencia.
Javier Hernandez was the next player to be struck down, hurt early on after being tackled by Jonathan Woodgate and subsequently withdrawn and replaced by Michael Owen in the 11th minute.
Penalty shout: Javier Hernandez was taken out by Jonathan Woodgate
Ferguson said: 'It is not easy. With Hernandez he gives you that penetration and speed. That was a loss.
'Jonny got an ankle injury in training. We had a nightmare of a training session yesterday - Michael Carrick, Wayne Rooney, Jonny Evans.
'Jonny thought he would be okay but in the warm-up it was no use. We had to make that change.'
Despite the setbacks, United took the lead in the 27th minute when Nani played a one-two with Darren Fletcher, cut into the box and clipped the ball past Asmir Begovic.
David De Gea then produced superb saves to deny Andy Wilkinson and Jon Walters before the hosts equalised, Peter Crouch notching his first Stoke goal by heading in Matthew Etherington's corner seven minutes into the second half.
Crouch caused problems for United throughout the contest and Ferguson suggested the tall frontman was getting away with committing infringements.
Crocked: Hernandez was replaced by Michael Owen
Ferguson said: 'He fouls all the time. He gets off with it because of his height but he jumps on top of defenders all the time.
'He has been doing that for a long time. Referees know that. Even with the goal he has maybe caught Phil Jones, but he is right above him.
'He is a handful in the air, there is no doubt about that.'
Ferguson was keen to praise De Gea, who looked unconvincing at times when high balls came into the box but certainly demonstrated his shot-stopping prowess.
'He made a great save in the first half, knocked it round the post,' Ferguson said.
'He was very confident. He sailed through and showed terrific composure. Nothing disturbs him.'
The result meant United leapfrogged Manchester City to return to the top of the table, but they are only ahead of their derby rivals - who earlier beat Everton 2-0 - on goal difference.
It was also just deserts for Stoke after the performance they put in, and overall Ferguson felt a draw was fair outcome.
'There are two parts to it,' Ferguson said. 'One, they keep you under pressure. In the main, we have dealt with that quite well.
Equaliser: Peter Crouch rises to head home his first goal for Stoke
'As expected, if they were going to score, it was going to be from a set-piece. They have so many big lads in their team and they do keep you under pressure that way.
'In terms of the attacking part, we showed some good play and maybe should have scored more than the goal we did.
'A draw is probably a fair result. It is a difficult place to come to.
'We have always done well here, but maybe making the changes we had to unshipped us for parts of the game.
'I was pleased with the performance. They battled really hard and played like real champions in every sense of the world.'
Stoke had lost all six of their previous Premier League meetings with United and Potters assistant manager Dave Kemp was pleased to see the sequence halted.
'It's a great result for us and the first time we have taken anything off Manchester United,' Kemp said.
'They were the last team in the Premier League that we haven't got anything against.
'Having played very well on a number of occasions against them without getting anything, today we did and we are delighted.'
Tweet and sour for Rooney as he misses Stoke game through injuryStoke 1 Man United 1: Crouch nets first Potters goal to deny United victory after Nani wonder strike