Pele, who won three World Cups, insisted Messi, yet to taste meaningful senior success with his country, should return to the international stage.
And, after the 29-year-old missed a crucial penalty in his side's shootout loss, the Brazilian suggested the error could have been made by any player.
"In the last 10 years, no doubt he was the best player. What happened to him happens in football. Only the one who kicks the penalty can miss the penalty," Pele was quoted as saying by Sky Sports.
"He got very upset but maybe [he should] wait a little bit and he'll forget because this has happened with a lot of good players. A lot of good players have missed penalty kicks.
"The last 15 years, for me, he was one of the best players in the world and this is more important."
Messi's friend, Argentina squad masseur Marcelo D'Andrea, is confident Pele's wish of seeing the superstar forward back in an Albiceleste shirt will be granted.
"I have no doubt that [Messi] will play the World Cup," he told FM Pop. "I have great faith, but I must leave him alone and trust in his silence.
"He loves the national team, and gives everything for his country."
D'Andrea added that Messi's announcement came as a surprise to the staff and his team-mates, as the player had made no mention of his intentions.
"When I went to get on the pitch there was no consoling him," he added. "It was a harder blow to Messi with the national team, I have no doubt.
"His look at me killed me. I said, 'Come on, that's it.' He looked at me and left. Those things - you are carrying them for life.
"Nobody knew anything about the resignation of Messi. He said nothing in the locker room. We learned from the interview."