Walcott's omission from the final 23-man squad came as a major surprise and, as England struggled to find a cutting edge in South Africa, Messi feels having the Arsenal attacker on the bench would have proved a major advantage for England.
"I must say that at the time I thought it was a bad decision to leave Theo Walcott at home, and I think that has been proved right," he said in the Star. "I can only speak from experience but he was one of the most dangerous players I have ever played against."
During last season's Champions League quarter-final at Emirates Stadium, Walcott came on as a substitute as Arsenal trailed Barcelona 2-0. His goal sparked a comeback that led to a 2-2 draw in the first leg, and Messi says his team-mates identified him as a key threat for the return.
"Barcelona players are not scared easily but I can tell you that when we played Arsenal last season he truly worried us," he said.
"When we were playing Arsenal at the Emirates, we were so in control of the game at 2-0 - with all respect, Arsenal were not even in the game - then Theo came on and changed the game. He pretty much single-handedly salvaged a draw against Barcelona that night.
"Even in the return leg, our manager Pep Guardiola was telling us he was the player to watch out for, and the best players in the world like Xavi and Gerard Pique were telling us to watch out for him. The truth is that he really rattled him.
"If he could do that against Barcelona, think what he could have done against Germany and Algeria. Even if he didn't start, he would still have been very important for England.
"Along with Cesc Fabregas and Sergio Aguero, he would have been the best impact player at the World Cup."