Messi helped set up the South American side's winning goal in a tense 1-0 quarterfinal victory at Estadio Nacional, with many now believing this is the little maestro's tournament to lose following Neymar's tournament-ending injury and Cristiano Ronaldo's early elimination.
Wilmots, however, claimed he was not convinced by Argentina's performance despite its victory and insisted it was aided by a series of refereeing decisions that went in Messi's favor.
"We were not impressed by Argentina, absolutely not," said Wilmots, whose side beat the United States 2-1 in extra time on Tuesday. "It's just an ordinary team.
"I think that Messi is the star striker, star player, he never loses the ball. But I noticed a couple of fouls and the referee is never against him. I am noticing every time there is a little foul it is always in favor of Argentina.
"If we could have equalized in the last few seconds, Argentina is dead. They are finished."
Gonzalo Higuain's eighth-minute goal, with Messi playing a crucial role in the buildup, was enough to separate the teams, and Belgium was unable to find a way through the tight Argentine defensive line in the second half.
Wilmots criticized what he perceived as his opponent's negative approach as it attempted to close out the game. The tactic allowed Argentina to clinch its first World Cup semifinal spot since 1990 when it went on to lose to West Germany in the final.
"I was wondering who was the favorite, who was making the game – Do you think Argentina played a good match today?" Wilmots said to reporters.
"We've seen the experience of Argentina. They can distort the rhythm of the game. It takes them 30 seconds to do a throw-in and the referee does nothing. They can break our rhythm and speed.
"The world has been able to see that Belgium has an excellent team. I think we can be proud of our team. Our opponent didn't give us any space and this was a quarterfinal of a World Cup. The details make the difference in a game but there was [no difference] in terms of quality."
However, Argentina coach Alejandro Sabella was delighted with his team's performance and urged it not to be satisfied with merely reaching the semifinals.
Argentina will play the winner of Saturday's second quarterfinal between the Netherlands and Costa Rica in Sao Paulo on Wednesday. Sabella believes his team has a strong chance to win the trophy for the third time in its history.
He reserved special praise for Messi, despite his superstar failing to get on the scoresheet.
"I felt that Messi played a wonderful match," Sabella said. "It is not just about scoring, but attracting three opponents to him and then giving it to a teammate. Every move he makes is a sign of hope for us and endangers the opponent.
"He almost never loses the ball and it is like water in the desert for us. He gives us that. Today, when it was dry. He gave us that breath of fresh air every time he held the ball and that is something we truly value."
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- Lionel Messi