Despite past clashes over discipline, Martinez insisted he took what he knew was an unpopular decision for the good of the team.
"Very reluctantly my international career comes to an end," the 29-year-old Nainggolan wrote in English on Instagram an hour after Martinez made public a decision which he had broken to the player in person the night before in Rome.
Martinez said his offensive strategy since he took over following the team's Euro 2016 disappointment no longer offered a role to Nainggolan, despite his huge part in Roma's charge to the Champions League semi-finals this year.
The player himself, who also announced plans to retire last year after Martinez left him out, made clear he saw a clash of personality as an issue.
"I’ve always done everything I could to represent my country. Being yourself can be bothering," he said.
In his native Dutch, he said; "Unfortunately, being REAL is not enough for SOME PEOPLE", adding that the decision to quit international soccer gave him "much pain in my heart".
Martinez, who also sprung a surprise by not naming his final 23-man squad, declined to give details of what he called an "honest" talk with the player, who cemented his popularity among fans at Euro 2016 where Belgium reached the quarter-finals.
But his decision was tactical.
"We know that Radja has a very important role in his club and we cannot give him that role in our squad," Martinez told a news conference."
Contrary to expectations, Martinez listed 28 players on Monday. These will be whittled down to the final 23 for Russia on June 4, two days after a friendly against fellow World Cup finalists Portugal in Brussels.
Giving himself an extra couple of weeks until FIFA's last squad deadline would give the likes of experienced Barcelona defender Thomas Vermaelen time to prove his fitness.
Third in the world rankings and hungry for the success that has eluded them despite boasting some of Europe's most gifted players, England's Group G opponents head to Russia with Premier League stars including Chelsea forward Eden Hazard and midfielder Kevin De Bruyne from champions Manchester City.
Manchester United striker Romelu Lukaku also makes the preliminary squad despite recent injury issues, along with 32-year-old Manchester City skipper Vincent Kompany in defence.
Among fresher faces given a chance are winger Adnan Januzaj from Real Sociedad and 21-year-old Monaco midfielder Youri Tielemans.
The 28-man provisional squad:
Goalkeepers: Thibaut Courtois (Chelsea), Simon Mignolet (Liverpool), Koen Casteels (VfL Wolfsburg), Matz Sels (Newcastle United/Anderlecht).
Defenders: Toby Alderweireld (Tottenham), Christian Kabasele (Watford), Jordan Lukaku (Lazio), Thomas Meunier (Paris Saint-Germain), Thomas Vermaelen (Barcelona), Jan Vertonghen (Tottenham), Laurent Ciman (Los Angeles FC), Dedryck Boyata (Celtic), Vincent Kompany (Manchester City)
Midfielders: Marouane Fellaini (Manchester United), Axel Witsel (Tianjin Quanjian), Kevin De Bruyne (Manchester City), Eden Hazard (Chelsea), Nacer Chadli (West Bromwich Albion), Leander Dendoncker (Anderlecht), Thorgan Hazard (Borussia Moenchengladbach), Adnan Januzaj (Real Sociedad), Youri Tielemans (Monaco), Mousa Dembele (Tottenham Hotspur).
Forwards: Michy Batshuayi (Chelsea/Dortmund), Christian Benteke (Crystal Palace), Yannick Carrasco (Dalian Yifang), Romelu Lukaku (Manchester United), Dries Mertens (Napoli)
(Reporting by Alastair Macdonald, editing by Ed Osmond)
