But Canadian captain Christine Sinclair did not make the women's shortlist.
The women's final three consists of Americans Abby Wambach and Alex Morgan and Brazil's Marta, a five-time winner.
The men's finalists were picked from a list of 23 candidates, with Messi looking to become the first player to win the award four times. The Argentina playmaker won the award last three years.
"I think they are perfect picks. There is no doubt these players are among the best," said former Brazil great Ronaldo, a three-time award winner. "Messi and Ronaldo are really the only ones with a chance of winning, that's how it's been recently."
The winner will be announced in Switzerland on Jan. 7. The only two other players to have won the FIFA award three times are Ronaldo and former France great Zinedine Zidane.
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 be presented to Radamel Falcao, Neymar or Miroslav Stoch.
The omission of Sinclair from the women's ballot is worthy of debate, given her star-making performance at the London Olympics.
The talismanic captain led Canada to a bronze medal at the Games, scoring a hat trick in a 4-3 extra-time semifinal loss to the U.S. Her 143 career international goals rank third all-time, second among active players behind Wambach (148).
Morgan and Wambach are looking to win the women's award for the first time after leading the United States to its third straight Olympic gold medal in London. Wambach made the shortlist last year, finishing third in the voting. The U.S. team also is represented by Swedish coach Sundhage, who led the team to the gold at the 2012 Games.
"Women's football was at its best this year," Blatter said, noting the record crows attending the matches at the London Games.
Marta is looking for an unprecedented sixth award.
"It's a great honour to be in the running again," Marta said. "It's going to be a very tight dispute and I'm sure the winner will be very deserving."
The 25-year-old Messi earlier 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, along with Xabi Alonso, Karim Benzema, Iker Casillas, Mesut Oezil and Sergio Ramos. In addition to Messi and Iniesta, the 23-player list also included Barcelona players Xavi Hernandez, Gerard Pique and Sergio Busquets.
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 also 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, along with Casillas and Manuel Neuer of Bayern Munich.
FIFA President Sepp Blatter said it is difficult for players outside of Europe to win the top award.
Blatter made the comments after praising the 20-year-old Neymar, who is touted as the future of Brazilian football. Neymar has a contract with Santos through the 2014 World Cup and has turned down several offers to move to Europe, including one from Chelsea.
"It is difficult," Blatter said. "All the focus is in the big European leagues. And this is the market today in football. It is the benchmark of club football."
Neymar won the 2011 goal of the year award and is looking to retain the prize courtesy of his goal for Santos against Internacional on March 7, when he scored following a maze of dribbling from mid-field. Falcao is in the running for his overhead kick on May 19 in Atletico Madrid's game against America de Cali, while Stoch is in the final list for his superb hook shot from the edge of the box for Fenerbahce on March 3.
Voting is by national team coaches and captains, and journalists invited by co-organizer "France Football" magazine.
— With files from The Canadian Press
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