The match, a Belgian home fixture was moved after the city of Brussels deemed it “impossible to organise this very high-risk match” in the city due to tensions linked to the Israeli-Palestinian conflict.
Other Belgian cities also refused to host the match.
De Bruyne gave Belgium a 21st-minute lead. Jeremy Doku broke down the left and pulled the ball back to his unmarked Manchester City club-mate.
Israel levelled after 36 minutes when Timothy Castagne deflected a header powerfully off his own crossbar and into the net.
Youri Tielemans ran onto a flick from Lois Openda to put Belgium ahead again in the 48th minute.