Messi scored four goals in the group stages, but, other than a strong first-half showing against Belgium, the Barcelona star failed to live up to his billing in the knockout phase.
The Argentina captain missed a good chance to win the final in the Maracana in the second half, dragging his shot wide when through on goal.
And FIFA president Blatter conceded he was surprised FIFA's technical study group had given the Argentina skipper the prize.
"I was myself a little bit surprised when I saw Messi coming up to collect the best player of competition," said the head of FIFA, who was handing out the awards in the stadium after the match.
Holland's Arjen Robben, Colombia striker James Rodriguez and now World Cup winner Thomas Muller were among the front-runners for the award.
"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)," Blatter added.
Maradona won the same accolade as Messi in 1986, but, unlike his compatriot, he left the tournament with a World Cup winners' medal around his neck.
The outspoken former Argentina skipper feels Messi did not deserve to win the award.
''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).''
Maradona was right, Messi could not have cared less about winning the Golden Ball - he admitted as much after the match.
"In these moments, the prize doesn't interest me at all," Messi said a few minutes after Mario Gotze's 113th-minute winner which decided the final in Germany's favour.
"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."
Messi was not the only man to miss a good chance in the Maracana on Sunday.
Messi wishes either he or one of his team-mates had found the net.
"They had more of the ball, but we had the better chances," he said.
"I think that at the end we didn't get the luck that we needed. The chances we created were clear.
"We had three clear ones - mine, the one of Higuain and Rodrigo, but we could not finish them. Now we have to move on."
Javier Mascherano admitted immediately after the match that he felt "immense pain".
But, after being given a few minutes to reflect on Argentina's first run to the final in 24 years, the Barcelona midfielder was a little more upbeat.
"We are out, but everything that we have been through in the last 34 days will help us keep growing," Mascherano said.
"As a group we are a unit, we are unstoppable and we have shown that.
"We were at a low but we ended up playing a World Cup final against Germany and we had a real chance of winning.
"The players have grown, they have developed out here. We all fought with our heart and we were just five minutes short. It will be hard for us to pick ourselves up after this. It's a big blow because we had it in the palm of our hands, but it's been a great World Cup."
- Sports & Recreation