Radja Nainggolan (Getty Images)
The heavily tattooed 30-year-old has played 30 times for his country and is popular with supporters, but his relationship with coach Roberto Martinez has often been strained.
The Spaniard flew out to Italy over the weekend to explain his choice.
The absence of Nainggolan, who scored twice for Roma in the second leg of the Champions League semi-final against Liverpool this month, was the biggest surprise in the 28-player list that will be reduced to 23 before the tournament.
Belgium face England, Panama and Tunisia in Group G at the World Cup.
"The reason is tactical. In the last two years the team has worked in a specific manner. Other players had those (midfield) roles.
"We know that Radja has a very important role in his club and we cannot give him that role in our squad."
Martinez added: "It was a sad and difficult decision. He is a player with a lot of class and he was voted Roma's best player, but I've made my decision for purely tactical reasons.
"I have put in place a specific system that works. I can't use Radja in a secondary role."
The decision to omit Nainggolan was criticised by former Belgian international Philippe Albert.
"We must be the only country in the world to be making the trip without one of the best players in the world. This is not the way to become world champions."
Nainggolan had earned 30 caps for Belgium since making his debut against Chile on May 29, 2009.