The Argentine forward had lost out to Cristiano Ronaldo for the FIFA Ballon d'Or the day before.
The UEFA team was chosen by users of the European body's website, and not a single Barca player was included despite the team winning the Spanish Primera Division title. Messi finished 13th in terms of votes, cast by more than half a million visitors to the website or via social media sites.
Only one current Premier League player, Arsenal's Mesut Ozil, has made it into the team, although Wales midfielder Gareth Bale, who moved from Tottenham to Real Madrid in the summer, is also included.
No English players made it into the team, but there are four from Germany - Manuel Neuer, Philipp Lahm, Marco Reus and Ozil.
Portugal captain Ronaldo, who won the Ballon d'Or on Monday, is named in the team for the eighth time and an unprecedented seventh time in a row.
The uefa.com team of 2013: Manuel Neuer (Bayern Munich and Germany); Sergio Ramos (Real Madrid and Spain), Thiago Silva (Paris St Germain and Brazil), Philipp Lahm (Bayern Munich and Germany), David Alaba (Bayern Munich and Austria); Franck Ribery (Bayern Munich and France), Marco Reus (Borussia Dortmund and Germany) Mesut Ozil (Arsenal and Germany), Gareth Bale (Real Madrid and Wales); Cristiano Ronaldo (Real Madrid and Portugal), Zlatan Ibrahimovic (Paris St Germain and Sweden).