FIFPro made the plea to UEFA in the wake of Bayern's David Alaba, Holger Badstuber and Luiz Gustavo and Chelsea's Branislav Ivanovic, Raul Meireles and Ramires all receiving booking in their respective semi-final second legs which rule them all out of the showpiece later this month.
The appeal did not cover the suspension of Chelsea captain John Terry, who received a straight red card in the second leg of the semi-final clash against Barcelona.
The union, based in the Dutch town of Hoofddorp, argued that the collection of a third booking in the competition for a player who could potentially have played 12 games should not warrant them missing them the final, calling the punishment "disproportionate".
Michael van Praag, the Dutch UEFA executive committee member who is head of the body's Champions League Rules group, was quoted on FIFPro's website saying: "We have just had three sessions with representatives of the European Clubs' Association and others, in which we confirmed the rule for the coming three years."
Van Praag added: "We did not receive any request whatsoever concerning the yellow card rule, not even from the representative of Bayern Munich. And so we will be continuing the rule for the next three years."
UEFA will wipe the slate clean for yellow cards after the quarter-finals in Euro 2012 but Van Praag defended the apparent inconsistency.
He added: "Different rules can apply in different competitions. The current rules are the result of a careful, democratic procedure."
This season's final will be held at the Allianz Arena, home ground of Bayern, on May 19.