The 33-year-old marked the passing of his legendary compatriot after scoring a goal as Barca claimed a 4-0 victory at Camp Nou.
Messi removed his shirt to show a jersey of his boyhood club Newell's Old Boys bearing the No.10, which Maradona wore during a brief stint toward the end of his career.
And he has subsequently fallen foul of rules forbidding the removal of shirts during games, despite Barca citing the player's desire to pay tribute as a mitigating factor.
Messi was also booked for the incident.
The Argentina international had also paid tribute to Maradona on social media, writing: "He has left us but he isn't going anywhere because Diego is eternal."