The Manchester United manager expected to have his star striker available for yesterday's 1-0 win over Liverpool at Old Trafford.
However, after experiencing discomfort with the ankle injury he sustained at West Bromwich on New Year's Day during training on Friday, Ferguson decided it was not worth risking the England forward.
Spurred on: Rooney is expected to return for the clash with Tottenham
Instead, he will have more treatment this week in a bid to be fit for the eagerly-awaited White Hart Lane encounter.
'I could have put him on the bench but there was no point,' said Ferguson. 'He just felt it again on Friday and when he came in on Saturday morning you could see there was a reaction. At that point, we said no.'
The United boss also expects skipper Nemanja Vidic to be fit, although Edwin van der Sar might need another week to recover from a flu virus that has laid him low for all three games in 2011 so far.
Thankfully for the Scot, his side were able to sneak past Liverpoolwithout that trio thanks to a controversial second-minute penalty fromRyan Giggs.
Taking no risks: Rooney missed out on the clash with Liverpool following a recurrence of his ankle injury
Although there was plenty of debate about what contact there had been from Daniel Agger to send Dimitar Berbatov tumbling in the first place, Giggs was not too concerned as he earned United a fourth-round trip to Southampton, with Ferguson adamant referee Howard Webb made the correct call.
'Dimitar says he was definitely clipped,' said Ferguson. 'The replay shows he was touched slightly but the momentum is enough to bring the player down. The referee was right.'
The United camp also felt Webb made the right decision in the other pivotal moment of the game, when Liverpool skipper Steven Gerrard was sent off for a first-half lunge on Michael Carrick.
'There was no doubt,' argued Ferguson. 'It was two-footed and he was off the ground.
'Steven Gerrard is not that type of player but it was a reckless challenge. He didn't leave the referee with any option.'
Ferguson was delighted with the way his side controlled the remainder of the game, even if he was disappointed they were unable to build on their advantage against a Liverpool side still getting used to having Kenny Dalglish in charge for a second time.
'I didn't think I would see this day,' admitted Ferguson. 'When you have been out of the game so long you don't expect it to resurface again.
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