Spain coach Vicente Del Bosque, former Barcelona coach Pep Guardiola and Real Madrid coach Jose Mourinho were in the running for the world coach of the year award. The women's coach of the year award will go to either France's Bruno Bini, Japan's Norio Sasaki or the United States' Pia Sundhage.
The Puskas Award for the best goal of the year will go to Radamel Falcao, Neymar or Miroslav Stoch.
The 25-year-old Messi this year won his second Golden Boot award for scoring the most goals in Europe's domestic leagues last season. He has scored 82 goals this calendar year, putting him only three shy of Gerd Mueller's record.
Messi won last year's Ballon d'Or prize over Cristiano Ronaldo, who scored a team leading 46 goals last season for Real Madrid.
Cristiano Ronaldo, the winner in 2008, was one of the six nominees from Real Madrid, with Xabi Alonso, Karim Benzema, Iker Casillas, Mesut Oezil and Sergio Ramos. In addition to Messi and Iniesta, the 23-player list included Barcelona players Xavi Hernandez, Gerard Pique and Sergio Busquets.
"It's an honour and a source of pride for me to have been chosen as a candidate for both the Ballon d'Or as well as the Fifa ideal 11," Ronaldo said in a statement on Madrid's website. "They are both wonderful awards and I think that to be among the nominees is principally the result of hard work and the help of my teammates on Real Madrid and the national team."
Iniesta finished second to Messi in the 2010 vote.
Seven Spain internationals made the 23-name list and all three in the shortlist play in the Spanish league.
"This shows how strong the football is in Spain, not only in the clubs but also the national team," Fifa secretary general Jerome Valcke said. "We have a very strong [Spanish] football system in place."
Manchester City striker Mario Balotelli and Brazil forward Neymar were in the running. Manchester United striker Wayne Rooney was the only English player on the list, while United teammate Robin van Persie also was a candidate after being the Premier League's leading scorer last season for Arsenal. Juventus veteran Gianluigi Buffon was among the three goalkeepers in the list, with Casillas and Manuel Neuer of Bayern Munich.
- AP