The RFEF competitions committee fined the Barcelona star for removing his jersey after scoring in the fourth goal in a 4-0 win over Osasuna.
After a strike from outside the box, Messi removed his Barca shirt to reveal a Newell's Old Boys jersey emblazoned with Maradona's famous number 10.
After the game, Messi posted a photo of his tribute alongside an older image of Maradona in the same shirt, adding the message “Farewell, Diego” in Spanish.
Former Barca and Argentina great Maradona died last week at the age of 60 and was honored before all LaLiga matches over the weekend.
The RFEF also refused to rescind the yellow card that was shown to Messi for his goal celebration, and fined Barcelona €180 euros ($216).
Messi and the club can appeal the decisions.