The university side, held 0-0 by Guadalajara at their Olimpico Universitario ground in the capital in the Clausura championship, were celebrating the 50th anniversary of their promotion to the first division in January 1962.
"The reproduction, whether real or virtual, of representative logos or emblems of FIFA, confederations, member associations, leagues, clubs or other bodies is forbidden on the field of play, the goal nets and the areas they enclose," state the laws of world governing body FIFA.
A FMF statement said the "violation of FIFA's Laws of the Game 2011-2012 committed by Pumas club... will be forwarded to the Disciplinary Commission of the Mexican Football Federation... for its analysis and to determine a sanction."
The match was something of a damp squib with a defensive Guadalajara glad not to notch up a fourth consecutive defeat.
Guadalajara were under new coach Ignacio Ambriz, appointed during the week to replace Fernando Quirarte, who resigned after the Chivas lost their first three matches, their worst start to a championship.
Pumas coach Guillermo Vazquez said both sides were mostly concerned with not losing given the intense rivalry between teams from the capital and the western city of Guadalajara.
'IN DEBT'
"No one wants to lose these kinds of matches, both sides go into them concentrating on not committing errors and the fight [for the ball] in all parts of the pitch is very even," he told reporters.
Ambriz said: "I think both sets of fans are unhappy, what's important in football are goals, there weren't any today, perhaps we're in debt, let's hope we can improve."
Santos Laguna took a two-point lead in the standings with a 3-1 win at Tijuana.
Goals from Colombia's Darwin Quintero, striker Cristian Suarez and midfielder Juan Rodriguez sent Apertura championship runners-up Santos top with 10 points from four matches.
Argentine striker Jose Sand's had promoted Tijuana back in the game with a 55th-minute penalty but Suarez restored the visitors' lead within nine minutes.
Guadalajara's arch-rivals America won 3-1 at San Luis on Saturday with two goals from Ecuador striker Cristian "Chucho" Benitez, who also laid on the second for Brazilian midfielder Rosinei.
America are second with eight points, one more than a group of four teams including Tijuana and title holders Tigres UANL, who beat Santos in the Apertura final in the first half of the season.
Argentine striker Emanuel Villa scored both goals in Cruz Azul's 2-2 draw away to Atlante in Cancun, including a controversial 86th-minute equaliser which television replays confirmed he helped into the net with his arm.
