The Catalan giants were this week given a transfer embargo for the next two windows due to irregularities found in their dealings at youth level.
FIFA's disciplinary committee handed out the ban after Barca's case was examined by the Players' Status Committee, of which Jimenez is a member.
Jimenez has made it clear the decision had nothing to do with the club's rivalry and that the sanctions were not made by the panel he sits on.
"The Players' Status Committee to which I belong has no sanctioning power," he told Spanish newspaper AS.
"What we do is study the files we receive, but the sanction to Barca is the responsibility of the disciplinary committee of FIFA.
"Neither I nor Real Madrid have anything to do with the penalty.
"The big clubs are the first to collaborate with child protection, but unfortunately it is true that there has been marketing to minors and FIFA is worried about it."
Barcelona were charged with breaching rules relating to 10 signings between 2009 and 2013 at youth level, but the Camp Nou club have confirmed they will appeal the decision and could take it to the Court of Arbitration for Sport.
And Barca president Josep Maria Bartomeu believes the ban is "someone on the outside is trying to do damage to Barca".
