Chelsea host Wolverhampton Wanderers on Saturday and will expect to chalk up their fifth successive home league win, which would put them eight points ahead of United.
It emerged this week that the manager had known as early as August about Rooney's intention to leave and that distraction, combined with the poor form of the England striker - who is out this week with an ankle injury - can hardly have helped his team-building plans.
"We don't want this to carry on. We don't want it to become a saga," Ferguson said. "We've got the team to consider and an important game on Sunday.
"If we carry on talking about one individual, dominating all of the headlines and all of our thoughts, then we're not doing our job."
Ferguson rested Dimitar Berbatov and brought Javier Hernandez off the bench for the last 12 minutes of Wednesday's 1-0 Champions League win over Bursaspor but Federico Macheda did not exactly grasp his opportunity as he failed to spark in a lone striker's role.
With Ryan Giggs joining Rooney in the treatment room Ferguson has some juggling to do for what will be a real test of his side's mettle.
United, after drawing at Fulham, Everton, Bolton Wanderers and Sunderland this season, as well as being held at home by West Bromwich Albion last week, will travel nervously while combative Stoke will relish a chance to add to Ferguson's woes.
Hard on Chelsea's heels are Manchester City, who play third-placed Arsenal in an intriguing clash at Eastlands on Sunday.
Liverpool failed miserably to rise to the occasion of last weekend's Merseyside derby and were well beaten 2-0 by Everton.
