United face Cluj at home on Wednesday night in their final UEFA Champions League group game and top spot has already been assured.
Ferguson is expected to make several changes to his team for the game, but he is not intending to leave Rooney out ahead of the weekend's clash with local rivals Manchester City.
The United boss does not want the England international to lose any momentum after he missed the matches against Norwich City and Galatasaray last month due to illness.
And, having scored twice against Reading in the Premier League last Saturday, Ferguson wants Rooney to build on his 'best performance of the season'.
"When Wayne gets interrupted, he needs three games to get back," said Ferguson. "That's why he'll definitely play.
"Wayne needs to play a lot of games to get his match fitness up. He's a strongly-built lad and when he misses two games, it takes him three games to come back. It's the way he's always been.
"He'll play and hopefully that brings him on further. On Saturday [at Reading], that was his best performance of the season so far."