Messi received the prestigious Golden Ball accolade following Argentina’s 1-0 extra-time defeat to Germany in the final on Sunday.
FIFA president Blatter, who handed out the award, admitted he was surprised to see the Barcelona star chosen ahead of players such as James Rodriguez, Arjen Robben and Thomas Muller.
"I was myself a little bit surprised when I saw Messi coming up to collect the best player of the competition," said Blatter.
"If you compare the beginning of the tournament and why finally the Argentina team got into the final, they were decisive and I think it was a decision (based on that).”
Messi started the tournament well, scoring crucial goals in group games against Bosnia-Herzegovina, Iran and Nigeria, but struggled to replicate that form in the knock-out stages.
Argentinian icon Maradona knows what it takes to win the Golden Ball, having done so himself in 1986 when he inspired Argentina to their last World Cup title.
He was adamant his compatriot did not deserve to win it and suggested the decision was influenced by factors off the pitch.
"I would give heaven and earth to Leo, but when marketing people want him to win something he didn't (deserve to) win, it is unfair," Maradona said.
"I could see that he didn't want to go up and collect it (the award)."
Messi echoed that sentiment, admitting the Golden Ball was scant consolation for the heart-breaking defeat inflicted upon Argentina by Mario Gotze's 113th-minute winner.
"In these moments, the prize doesn't interest me at all," Messi.
"We wanted to take home the trophy and enjoy it with all the people in Argentina.
"It's very painful to lose in the manner that we did because we were so close to penalties."