"We have made good progress with the lad. The medical team have been fantastic but I'm not prepared to take a risk if the player isn't 100 percent fit," Ferguson told a news conference on Tuesday.
"We're looking at the Manchester City game (on April 17) and maybe Blackburn (on Sunday) as a substitute."
Reports in the British media on Monday had suggested the injured England player could make a surprise return at Old Trafford after suffering ankle ligament damage in Munich.
I don't think he will be on the bench (on Wednesday) although he might talk me into it, it is a difficult one," Ferguson added with a smile.
The 24-year-old, who had been ruled out for two to three weeks, did not take part in a training session on Tuesday.
Rooney was in top form before the injury, scoring 34 times in all competitions including the opening goal in United's 2-1 first leg defeat by Bayern.
He is a key member of the England team hoping to win this year's World Cup in South Africa.
Teenager Federico Macheda, who has been hampered by shoulder and calf injuries throughout the season, had been tipped to replace Rooney on Wednesday but Ferguson said the Italian striker would start on the bench.
"It's been a hard season for the boy... we've only had him back a month into full training with the first team. I don't see him starting but certainly he can play a part," said Ferguson.
"He's on his way back and the boy's a terrific talent."
United have defender John O'Shea available again after a leg injury. The 28-year-old has not played since sustaining a dead-leg in Ireland's World Cup playoff against France in November.
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