In other key friendlies, Spain cruised to a 5-0 win over Andorra, France beat Luxembourg 3-0 and Denmark got the better of Sweden 2-1.
De Bruyne fired home a long-range shot a minute before halftime to hand his side the lead after goalkeeper Matija Sarkic was left in no-man's land by a defensive mix-up.
It was a cruel blow for Sarkic, who had kept Belgium at bay for almost the entire half with a remarkable series of saves - notably from Yannick Carrasco, who had four clear chances to open the scoring.
Leandro Trossard tucked away a penalty with the last kick of the game to double the score.
Belgium have a second warm-up friendly, against Luxembourg in Brussels on Saturday, before heading to Germany next week.
Christian Eriksen scored a stunning late winner to give Denmark a 2-1 victory over Sweden in a lively friendly in Copenhagen.
It took little more than a minute for the home side to break the deadlock as Sweden's defence was caught napping at the game's first corner, Eriksen finding Pierre-Emile Hojbjerg at the near post for an easy finish.
Sweden struck back quickly through Alexander Isak, who collected a blocked shot from Jens Cajuste and slammed it past Frederik Ronnow in the Danish goal seven minutes later.
The 32-year-old Eriksen, who collapsed due to a heart attack on the same pitch in Denmark's Euro 2020 opener against Finland, pulled the strings throughout, and his curling, dipping strike in the 86th minute secured a well-deserved win.
Attacking midfielder Mikel Oyarzabal climbed off the bench to score three times in the second half and help Spain to a 5-0 win over Andorra in their penultimate warm-up game before the tournament in Germany.
Ayoze Perez and Ferran Torres scored Spain's other goals.Â
In Metz, France strolled to victory against Luxembourg through strikes from Randal Kolo Muani, Jonathan Clauss and Kylian Mbappe.
