The centre-half has nothing but praise for the England international and has stressed that the Bavarians must be at their very best in Wednesday's game in order to progress
The England international missed this weekend's 4-0 Premier League win over Newcastle United due to a toe problem, but is expected to be match fit in time for Wednesday's match.
"I don't think he will miss the return," Boateng told the Bayern website. "But if it’s true, it would certainly be a big loss for United.
"Rooney is the key man for United. He always makes himself available, he goes looking for the ball, he takes the free kicks and corners and he’s always good for a goal."
Boateng then went on to stress that Bayern must be at their very best on Wednesday in order to reach the semi-finals after last week's 1-1 draw at Old Trafford.
"Every player is already focused on Wednesday," the versatile centre-half stated. "We’re all concentrating very hard in training. We shouldn’t aim for a goalless draw and we don’t want to either.
"We know what we’re capable of, and we also know we’ll need a very, very good performance on Wednesday if we’re to go through."
Bayern will be without Javi Martinez and Bastian Schweinsteiger due to suspension, while Xherdan Shaqiri and Thiago Alcantara are unavailable because of injury.