The versatile defender or midfielder suffered the injury during last month's FA Cup Fifth Round victory over Reading.
"He's not fit," Ferguson told a news conference on Monday.
Jones put in a top-class performance in the first leg of the European tie last month, man-marking Real forward Cristiano Ronaldo during the 1-1 draw.
Ronaldo scored with a towering header but Jones was not to blame.
"His performance over there was absolutely excellent," Ferguson said. "It's a miss but we can't deem it as something we can't manage, we've got options."
Ferguson added that United's main task against Real would be to put in a strong defensive performance to keep a lid on any breaks by the Spanish visitors.
"It probably will be the key to the game," he said. "I believe they are one of the best counter-attacking clubs in Europe... we've got to find a way of coping with that but also having our own threat in an attacking sense also."
One of those attacking threats could come from midfielder Ryan Giggs, who will make his 1,000th professional appearance in Tuesday's match at Old Trafford.
"Tomorrow he will be involved at some point, whether it's starting or on the bench I haven't made my mind up but he will be involved and of course his experience of these occasions will be vital to us," Ferguson said.
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