The Portuguese believes Lionel Messi has been given deliberate publicity to be crowned the recipient of the honour, while he laughed off speculation surrounding his future
The Barcelona forward is the current favourite to win the individual accolade for a third successive year but will have to oust team-mate Andres Iniesta and Madrid's Cristiano Ronaldo, both of whom also made the final three-man shortlist.
When quizzed on his attacker's chances of winning the award after Madrid's 4-1 Champions League win over Ajax on Tuesday, Mourinho replied: "The Ballon d'Or has already been given.
"When the heads of football speak and make the campaign, there is nothing you can do."
He then reflected on his side's victory over the Dutch champions, which saw them qualify for the knockout stages of the competition, through goals from Ronaldo, Jose Callejon and Kaka but was that not enough to see them claim top spot in Group D.
"We have to respect everyone. Last year we broke the record of points in the group stage, and in this year's group of death have been second," he said.
"We wanted to be first but it has not been possible."
And when questioned on the possibility of switching to Paris Saint-Germain in the summer, Mourinho joked: "They say I'm going to Paris? And the Spanish press announces [on Tuesday] that [Carlo] Ancelotti will go to Real.
"Maybe we'll have an exchange between the two clubs. But Paris would be a good destination for ... our next Champions League game?"