Messi, who had gone back on his decision to quit the team following their Copa America final defeat in June, scored the only goal in a 1-0 home win over Uruguay on Thursday that sent Argentina to the top of the South American group.
However, the Argentina captain will not travel with the team to Merida where they face Venezuela in another round of regional qualifiers, coach Edgardo Bauza said on Friday.
"He won't be able to play, he has inflammation and still feels pain, we can't take risks," Bauza told reporters after training at the Argentine FA headquarters outside Buenos Aires.
The AFA confirmed the decision, announcing on its website (www.afa.com.ar) that it had been taken after tests on Messi's groin in the morning.
"He has been told to rest and won't play against Venezuela," it said, with media reporting that Messi would fly directly back to his club Barcelona at the weekend.
The decision was easier for Argentina to take before they face the weakest team in the group having bagged three points in Tuesday's win in Mendoza, where they played a man short for half the match after Paulo Dybala was sent off.
IMPORTANT MATCHES
“My groin is hurting a lot, from before this match,” Messi told reporters after the win. “I always want to be (in the team)... but there are also a lot of important matches coming up (for club and country).”
Messi explained why he had said he was retiring from international football after Argentina’s loss to Chile in New Jersey in which he missed their first penalty in a shootout.
“I didn’t deceive anyone in that moment,” he said. “I was very disappointed because it was a hard blow and I said that because that’s what I felt.
“But afterwards, seeing what this group (of players) is like, and with the affection of the fans, I reconsidered.”
It was Messi’s third defeat in a major final with Argentina in two years, including the 2014 World Cup final against Germany in Brazil, and fourth altogether.
Messi is now back gunning for a fourth World Cup appearance in Russia in 2018 with Argentina heading the 10-nation group with 14 points from seven matches.
The top four qualify for the tournament while the fifth-placed team goes into an inter-continental playoff for another place in the finals.
(Writing by Rex Gowar, editing by Ed Osmond and Ken Ferris)
