There was a global outcry from media and fans after Messi, 27, was given the award following the defeat of his Argentina side to Germany in the 2014 World Cup final in which the Barcelona star had failed to live up to expectations.
Previously the result of a poll between the world's press and FIFA's Technical Study Group, Messi's surprise win was the consequence of analysis by the latter body solely after football's world governing body changed the voting process for the tournament in Brazil.
Even FIFA president Sepp Blatter admitted he was surprised by the decision, which led to fans jeering when Messi walked up the steps to receive his award at the Maracana, but Houllier -- a respected member of the Technical Study Group -- feels the choice was fully justified.
"I understand that it has surprised, because everyone only remembers the second half of Lionel Messi in the final. We, the commission, we look at all the games, and we judge that he was the most important man for his team. He went to the final, which is one of the conditions for the attribution of the trophy," the ex-Liverpool and Aston Villa boss explained.
"Moreover, Messi was more than decisive in the first four games. In the semifinal against the Netherlands, he took the first penalty and scored. The analysis also takes into account the fact he was the captain of a united team. A team that played well together. That's something we hadn't seen for a long time from Argentina. He was more than key in the squad and the way it was set up. For me, he fully deserves the Golden Ball given he took his team through to the final."
Critics claimed Dutch star Arjen Robben or the tournament's top scorer, Colombia's James Rodriguez, would have been more worthy winners. Houllier, however, explained neither had had a realistic chance.
He said: "Robben was exciting and very good, but he didn't carry so much weight with the team. He didn't score in either the semifinals or the quarters. Even though he won the penalty against Mexico, he was much less influential in his team's play.
"James Rodriguez stopped too soon, just like Neymar or the other key player in the Albiceleste's performance, Angel Di Maria. Di Maria might have been a very serious contender had he been able to go all the way. He was excellent, and very creative."
Houllier added that Germany's Thomas Muller, who struck five goals, had pushed Messi for the tournament's top individual prize.
He said: "There was a competition between Muller and Messi, but I repeat, we looked at all seven matches. The final counted, but only at the same level as the other games.
"Given the whole of the World Cup, the commission was unanimous that Lionel Messi win the trophy. I think public option was 'biaised' by the anti-Messi strategies of opposing teams, which caused him a lot of problems. Despite that, he almost always managed to get himself out of them. But everyone is entitled to their opinion."