The Argentine allegedly hurled verbal abuse at the Malaga defender and, after they squared up, the Barcelona attacker was shoved to the ground.
Tensions overflowed late in the game when Weligton appeared to grab Messi by the throat, with the Argentine attacker subsequently falling backwards to ground.
Barca players were pleading with the referee to send the Brazilian defender off for his actions, though he only received a booking, but Weligton has hit back by insisting that Messi initiated the confrontation by hurling verbal abuse at him when they squared up in the 81st minute of the game.
“I tried to prevent him from passing the ball and, after the move finished, Messi turned to me and called me a son of a wh*re,” the veteran centre-back, 35, told Cope .
As well as Weligton going into the referee’s book, Gerard Pique was yellow carded for his over-the-top remonstrations for the Malaga man to see red.
Barca remain top of La Liga with 13 points after five games, ahead of second-placed Sevilla on goal difference, while Malaga are placed 10th with six points.