An error by Kevin De Bruyne and an inspired pass from Mohamed Salah ensured goals for Egypt, who narrowly missed out on World Cup qualification in March, as they posted victory in a stop-start affair in Kuwait City.
Mostafa Mohamed scored in the 33rd minute with a rasping short ball after De Bruyne had lost possession just outside his own penalty area to give Egypt a half-time lead.
This was doubled straight from the second half kick-off as Salah's clever pass caught out Belgium's static defence and Mahmoud Trezeguet finished off with his left foot on the counter-attack.
But Egypt held out for the win with Salah close to getting a goal of his own right at the end.
Belgium, who are second in the FIFA rankings and were semi-finalists at the last World Cup, made several switches but showed little rhythm and cohesion with captain Eden Hazard looking out of sorts.
They were able to get in some game minutes for veteran defender Jan Vertonghen, who had been an injury concern over recent weeks. He came on for the final 20 minutes.
Friday's match marked the end of pre-World Cup warm-ups ahead of Sunday's tournament start. Belgium meet Canada in their first Group F game on Wednesday.