The Argentine football legend was substituted in the 73rd minute after asking to leave the pitch, his hand on the back of his leg, and then went straight down the players' tunnel.
Messi's team, Miami, has not yet commented on the incident. Despite Messi having to come off, Miami won 6-4 against Philadelphia in the last match before the World Cup break.
The 38-year-old has not formally confirmed that he will participate in the World Cup, but is widely expected to be part of what would be his sixth World Cup.
Argentina will play their first group stage match against Algeria on June 17.
