Ivorian Bailly was sent off for violent conduct in the second leg of United's Europa League semi-final victory over Celta Vigo in May for his part in a melee in the final minutes of a 1-1 draw at Old Trafford.
He was suspended for the 2-0 win over Ajax in the final, but will now also miss a further two games - including the August 8 European Super Cup clash against Champions League winners Real in Skopje, Macedonia.
"It was a red card in a semi-final, I think the punishment of not to play the final is enough, it's a big punishment not to play the final, and I say that normally he would deserve a clean sheet and start the next season with a clean sheet and ready to play the Super Cup," Mourinho said.
"But now he's an important player for us who is not able to play the Super Cup and the first match of the Champions League group phase but not to play the Europa League final and the Super Cup is very, very harsh."
Mourinho was speaking to reporters in Washington, where Manchester United take on Barcelona on Wednesday in the International Champions Cup friendly tournament.
Transfer news - particularly frenzied speculation over the possible departure of Neymar to Paris Saint-Germain - has dominated Barcelona's swing through North America.
Mourinho, whose side have recently signed Victor Lindelof and Romelu Lukaku, said he still has some modest transfer goals, saying he'd like to add a midfielder and a winger.
Mourinho declined to name any targets, and admitted he might only get one new addition.
"Ed Woodward is in control," Mourinho said. "He did Lindelof and Lukaku. He knows that I would like two more players but he also knows that I have balance, I understand the situation, I understand the market and if my club is not able to do two players and just one then I will accept that as a consequence of the market now.
"Our relationship is good and I just wait for good news. For me, good news is to have the players, or in this case maybe just the player, as soon as possible to work together with the team as that is important."