There was a global outcry from media, fans and experts after Messi was given the Golden Ball following the defeat of Argentina in the World Cup final.
Diego Maradona and even Sepp Blatter were among the surprised critics, but Houllier, who is a respected member of the FIFA Technical Study Group, has now defended the decision.
"I understand that it has surprised, because everyone only remembers the second half of Lionel Messi in the final," he told Le Monde.
"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.
"Moreover, 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 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."
Houllier also explained why fan favourites Arjen Robben and James Rodriguez never really stood a chance and that Thomas Muller had pushed Messi for the prestigious award.
"Robben was exciting and very good, but he didn't carry so much weight with the team. He didn't score in either the semi-finals or the quarters. Even though he won the penalty against Mexico, he was much less influential in his team's play,” he added.
"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."
“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 'biased' 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."
Previously the result of a poll between the world’s press and FIFA’s Technical Study Group decided on the Golden Ball winner, while Messi’s 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.