The prize, awarded for the first time last year to Barcelona forward Messi, is determined by votes from sports journalists from across Europe and was introduced as a replacement for the Ballon d'Or when the prestigious honour was absorbed into FIFA's World Player of the Year award in 2010.
Messi - who also won the final Ballon d'Or in 2009 and FIFA's awards in 2009, 2010 and 2011 - is a leading contender once again having scored a remarkable 73 goals in 60 games for Barcelona last season as he broke the club's all-time scoring record.
However, he only won the Copa del Rey, while his great rival Ronaldo, winner of the 2008 Ballon d'Or and FIFA World Player of the Year award, helped Real Madrid to the Liga title while scoring 60 goals in all competitions.
Though he possesses a lower profile than La Liga's two most prolific players, Barcelona midfielder Iniesta makes the three-man shortlist having helped Spain record a third successive victory in major international tournaments when triumphing at Euro 2012.
Iniesta was named Player of the Tournament following the finals in Poland and Ukraine and UEFA has disclosed that Italy midfielder Andrea Pirlo, beaten in the final in Kiev, came fourth in the vote to determine the Best Player in Europe award.
Spain's Xavi and Iker Casillas, former Chelsea striker Didier Drogba, Chelsea goalkeeper Petr Cech, Atletico Madrid striker Falcao and Germany and Real Madrid playmaker Mesut Ozil completed the top 10.
Bangor City's Les Davies, a shock inclusion on the long list announced on July 16, did not make the shorter version.
The prize will be awarded in Monaco on August 30 when the Champions League group stage draw is made. The 53 journalists will conduct a live vote and decide between the three Liga stars.