The developmens follow Wednesday's ill-tempered La Liga match with Villarreal.
Pepe, who was not sent off during the match, has been punished by the Spanish Football Federation's competition committee for comments directed at referee Jose Luis Paradas Romero following the final whistle at El Madrigal.
Mourinho has also been punished after being sent to the stands during a three-minute spell after Madrid had conceded a late equaliser which also saw Ozil and defender Sergio Ramos sent off.
Germany international Ozil was shown a straight red card for dissent while Ramos was given a second yellow card for his challenge on Nilmar, although the Spain defender has escaped a suspension after having the first of his two yellows cards in the game rescinded.
Rui Faria, a member of Mourinho's coaching team, was also given a two-match ban today following his dismissal from the bench just after half-time during the 1-1 draw.
The suspensions mean Pepe and Ozil will both have to sit out this weekend's league visit of Real Sociedad, as will midfielderLassana Diarra following his booking against Villarreal.
Also, Mourinho and Faria will be unable to take their places in the dugout.
Wednesday's match was the second time in four days Madrid had conceded a late free-kick to be held to a 1-1 draw, following last weekend's home game with Malaga, as their 10-point lead over Barcelona at the top of the standings was reduced to six.