The FIFA president has also expressed his sympathy for Luis Suarez following the Uruguayan's four-month ban for biting.
Messi was awarded the Golden Ball following Argentina’s 1-0 defeat to Germany in the final Sunday after he scored four goals in the tournament but failed to register a strike in the knockout stages.
“I was a little bit surprised when I saw Messi coming up as the best player in the competition,” Blatter said in a post-tournament news conference at the Maracana.
Suarez was banned by FIFA’s disciplinary for biting Georgio Chiellini during Uruguay’s victory over Italy in the group stage.
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An appeal was dismissed last week to get the new Barcelona man’s four-month ban reduced, but Blatter hopes to see the 27-year-old back to his best now he has moved to the Camp Nou.
Blatter said: “Concerning the Suarez matter I feel for him that such a punishment hurts. But as the president of FIFA I have to accept the decision of the committee.
“This player will come back to football on the pitch and what he has shown on the pitch. We saw his tactical and technical capacity and his smell for goal. I hope he will be back. He is now at one of the greatest clubs in the world.”