The decision to rest Messi proved costly as Atlanta United beat Inter Miami 5-2.
Miami coach Gerardo "Tata" Martino said the decision to hold out Messi was "because he has muscular fatigue and it was prudent to leave him out."
Atlanta United owner Arthur Blank said the FieldTurf at Mercedes-Benz Stadium, a surface viewed by some players as more taxing on their bodies than grass, was not the reason Messi remained in Miami.
Blank referred to Messi's statement after signing with Inter Miami that he wouldn't avoid playing on an artificial surface.
"I think he made that decision," Blank said.
"I don't really have an opinion on that. I'd just repeat what he said in his press conference, that he has competed on artificial turf since he was a youngster and to some extent as a professional. I don't think it had anything to do with his decision. I think he suffered some sort of injury, however minor it might be."
Atlanta United coach Gonzalo Pineda said he learned about Messi's decision on social media.
"I checked the Twitter account to know he was not coming," Pineda said, adding he encouraged his players to remain focused despite the attention given to Messi's status.
" I told the players, there are a lot of things out there in the atmosphere and everything seems to be about Inter Miami. We have to turn that to about us."
Messi's absence for the Major League Soccer match was a disappointment for a crowd of 71,635 at Mercedes-Benz Stadium.
Many fans wore pink Inter Miami shirts with Messi's name on the back. Flozel Marriott, a native of Jamaica and Atlanta resident who previously lived in Miami, attended the game with his wife, daughters and nephew. All wore Messi jerseys, though he said he otherwise supports Atlanta United.
"I was an Argentina fan growing up and I've always been a fan of Messi," Marriott said.
"I'm an Atlanta fan as well, but today I'm here supporting Messi. I want my children to see a legend."
Marriott was surprised to hear Messi would not attend the game.
"No, I did not know that," Marriott said, looking at his family.
"If he's not, they're going to be disappointed. That's where we spent all the money, just to see him."
Messi watched from the bench on Tuesday in Argentina's World Cup qualifying win at Bolivia. Argentina manager Lionel Scaloni said Messi was not feeling well.
Martino said on Friday he will avoid overworking the 36-year-old Messi during a busy portion of the team's schedule.
"We will be careful with him because we have a lot of important games in a short span. This is something that we knew would happen at some point," said Martino, the former Atlanta coach.
Miami next play a home game against Toronto on Wednesday and in Orlando on September 24.
(With AP inputs)