Gerald Houllier, who is a member of the FIFA technical committee, has explained why Messi was given the Golden Ball award.
I know a lot of us was very surprised when Messi was handed the award and a lot felt that Messi didn't deserve the prize, but here is what Houllier had to say about the award.
Mundo Deportivo reports Houllier saying:
I understand you all are surprised as you only remember the second half of Lionel Messi in the final. We committee looked at all three games and judged who was most important for their team. He also played in the final, which is one of the conditions for the award of the prize. Messi was more than decisive in the first four games. In the semi-final against the Netherlands he took the first penalty and scored. The analysis takes into account tat he was captain of a united team that played well together. That's something not seen in a while for Argentina. Messi was more than key in the national team and the way he played. To me, he fully deserves the Golden Ball award and he led his team to the final."
The Barcelona forward scored four in three group games but didn't find the target again in the tournament as Argentina finished as runners up.

http://dayosports..com/2014/07/why-i-gave-messi-golden-ball-houllier.html