The Barcelona superstar was caught mouthing “f*** off, the c*** of your mother” in the vicinity of official Dewson Silva.
But Messi, who missed the defeat to Bolivia as Argentina slipped out of the automatic qualification places, denies they were intended for Silva.
“My comments were never directed at the first assistant, they were comments made to the air,” Messi said, according to the Argentinian Football Association.
Argentina now face missing their first World Cup since Mexico 1970, with Messi due to miss three of the last four games.
With Messi in the team, Argentina have won five of six World Cup qualifiers – a return of 15 out of 18 points. While the two-time World Cup winners have won just twice without him – taking seven points from a potential 21 available.
With five games remaining and Messi only able to feature in the final game away at Ecuador – a very tough game in its own right – Argentina find themselves in big trouble. They sit third in CONMEBOL qualification on 22 points, just two points away from both Ecuador and Chile in fifth and sixth place.
By continuing to take 33.3 percent of points without their captain, Argentina would find themselves on 26 points upon Messi’s return and facing a first World Cup at home since Mexico 1970.
Messi was handed a four-game ban and fined 10,000 Swiss Francs (£8,111) after a foul-mouthed rant at an assistant referee in Argentina’s World Cup qualifier vs Chile.
The Barcelona superstar will miss Tuesday’s game vs Bolivia and three more vital qualifiers for Russia 2018 after video footage was brought to the attention of CONMEBOL and FIFA.
Messi, 29, was furious with official Dewson Silva during the first half of the 1-0 victory, and was seen on camera verbally abusing Silva, reportedly declaring: “f*** off, the c*** of your mother.”
Messi refused to drop the issue as the official joined the rest of his team in the centre of the field at the end of the game.
Messi was again in discussion with the officials and actively avoided shaking the hand of Silva. Brazilian referee Sandro Ricci subsequently pointed Messi towards the tunnel as the five-time Ballon d’Or turned shaking his head at the assistant.
A statement from FIFA read:
“The FIFA Disciplinary Committee, pursuant to articles 77 a) and 108 of the FIFA Disciplinary Code (CDF), took the following decision regarding the case of Argentine footballer Lionel Messi after an incident that occurred during the qualifying match of The FIFA World Cup Russia 2018 played between Argentina and Chile on March 23, 2017.
“Footballer Lionel Messi is considered guilty of having violated art. 57 of the CDF when pronouncing injurious words against an assistant referee.”
The incident was not included in the officials’ original report, but was added on Monday and sent to CONMEBOL – South American football’s governing body.
They then appealed to the Argentine FA on Monday afternoon for full clarification of the facts.
Argentine Football Association vice-president Armando Perez discussed the matter on Monday evening, telling La Tercera: “If he behaved out of place, then he should be penalised like any other player.
“He should not get a different deal just because he is the best player on the planet. It seems to me that he is in a position to be investigated.
“CONMEBOL is asking for all of the information. Everything that we know must be passed on.”