Alaba has received abuse online for ignoring Benzema in favour of the Paris Saint Germain superstar.
Messi was crowned FIFA Men's best player for 2022 at an awards ceremony held in Paris on Monday.
As captain of his national team Austria, Alaba was entitled to take part in the voting process and the Real Madrid defender chose Messi for his first vote, Benzema second and Mbappe third.
The 2022 awards took into consideration performances between August 2021 and December 2022, during which Alaba and Benzema won La Liga and the Champions League with Real Madrid while Messi won the Ligue 1 title with PSG and the FIFA World Cup with Argentina.
Benzema also won the Ballon D'or last year.
Alaba has explained his vote as a team decision by Austria and not his personal choice.
"Regarding FIFA The Best Award: The Austrian national team vote for this award as a team, not me alone," Alaba clarified on Twitter.
"Everyone in the team council is able to vote and that's how it's decided.
"Everyone knows, especially Karim, how much I admire him and his performances and I have often said that for me he is the best striker in the world, and that is still the case. Without doubt."
