Clearly upset by the chants, Rooney angered his once loyal supporters by kissing his United badge and signalling to the travelling fans.
Ferguson reacted by swiftly substituting Rooney and replacing him with Nani.
"I don't know why he was booked," Fergie told Sky Sports.
"The crowd obviously got him booked but the way the referee was behaving, I feared he may be sent off, for no reason of course.
"The way the crowd was reacting, getting him booked in the first place, I just felt I had to take him off."