The Spain international was one booking away from a one-match suspension and picked up that yellow when spending an extended amount of time taking a throw-in.
As a result, Carvajal will miss the dead-rubber against Borussia Dortmund in the final round of group-stage matches - with Madrid having already qualified for the knockouts - meaning he would have been available for the last-16.
However, the defender may now miss both legs of the first knockout rounds as UEFA have issued the Spaniard the charge.
UEFA's disciplinary panel will judge the case on Thursday, December 7, the day after the clash against Dortmund.