Centre half Leonardo Bonucci split the Belgium defence with a pass into the penalty area from just inside his own half and man-of-the-match Emanuele Giaccherini supplied a ruthless finish to put Italy in front after 32 minutes.
"If you're able to play an assist from 40 meters and you've got three centre backs there, there shouldn't be any danger so there's been a breakdown in communication which shouldn't happen at the top level," Wilmots told a news conference.
While praising the contributions of midfielder Marouane Fellaini and defender Thomas Vermaelen, he said striker Romelu Lukaku "didn't have a particularly happy night and ... De Bruyne could do better too".
Pressed about the form of the Manchester City midfielder, Wilmots added: "If I had an explanation I'd give you one. Is the kid tired after a busy season? Yes, perhaps. He's been training not quite at full pelt.
"(But) I think Kevin has given so much over the last four years for the national team, you shouldn't expect me to slate him."
After a spell at number one in the FIFA world rankings, Belgium went into Euro 2016 among the favourites. However, they find themselves bottom of the group after the other two teams, Ireland and Sweden, shared a 1-1 draw on Monday.
Wilmots' men, now ranked second in the world, managed just two attempts on target and, for much of the game, were reduced to long-range efforts that flew wide or were charged down by a packed Italian defence, before the Azzurri broke away late on score a second through Graziano Pelle.
"We need to really club together for the next two matches," added Wilmots, starting with Ireland on Saturday.
Defender Jan Vertonghen said: "We're in a very difficult position now, there's a lot of pressure on us. Most of all we need to make sure we take our chances.
"It hurts when you don't. I'm sure we have a squad that can cope. We will be ready."
(Editing by Tony Jimenez)
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