Zlatan Ibrahimovic and Cristiano Ronaldo were picked as forwards in the team which was dominated by players from the Bundesliga and La Liga.
Arsenal's Mesut Ozil was the only current Premier League player to make the line-up and there were none at all from Serie A.
UEFA said that 6.3 million people cast votes in the poll on its website. Real Madrid and Portugal forward Ronaldo was included for a record seventh successive year while Paris St Germain's Brazilian Thiago Silva was the only non-European.
It is the first time since 2007 that Messi has not made the team.
UEFA Team of the Year
Goalkeeper: Manuel Neuer (Bayern Munich)
Midfielders: Marco Reus (Borussia Dortmund) Mesut Ozil (Real Madrid/Arsenal), Gareth Bale (Tottenham Hotspur/Real Madrid), Franck Ribery (Bayern Munich)
Forwards: Cristiano Ronaldo (Real Madrid), Zlatan Ibrahimovic (Paris St Germain)