The first effort on goal came courtesy of Jeremy Doku, playing through the middle amid continued doubts over the match fitness of Romelu Lukaku, but it did not unduly trouble Dominik Livakovic.
Croatia worked a better early opening when Luka Modric picked out Petar Musa on the break, yet the FC Dallas forward could only find the side netting as the angle rapidly closed.
The Red Devils then drew a promising free-kick through Doku, although Maxim De Cuyper’s decision to take over duties from Kevin De Bruyne seems unlikely to be repeated in a hurry.
Sure enough, a quick De Bruyne free-kick started the move that led to the Belgium opener, and it was no surprise that Doku was heavily involved too. Tormenting his marker out wide, he worked the space to find a cross, and a defensive mess in the middle saw the ball fall to Youri Tielemans to slot home.
That was a fair reflection of the first half, although Thibaut Courtois had to be at his best to deny former club teammate Modric an equaliser just before the break.
Both teams came out unchanged for the second half, but they almost seemed to be killing time ahead of the expected mass switch in personnel.
That eventually came around the hour mark, with the hosts making five changes at once, and Ante Budimir came agonisingly close to an instant impact when his header crashed off the crossbar.
The same story then played out at the other end, with Hans Vanaken nodding his effort onto the woodwork following his introduction from the bench.
With the game seemingly petering to a close, fellow substitute Lukaku restated his credentials for a WC starting spot despite limited minutes at club level, settling the contest with a well-taken goal on the break in his first Belgium match in a year.
Zlatko Dalic’s side have now suffered consecutive friendly losses for the first time in two decades, having previously gone nine games in a row without defeat.
Next up for Belgium is a home friendly against Tunisia, ahead of a WC opener against Egypt. Croatia will begin their tournament in the USA with a massive clash against England, after they host Slovenia in their final preparation match.
Flashscore Man of the Match: Youri Tielemans (Belgium)