Jordan Pickford and Dominic Calvert-Lewin picked up their 29th and fifth England caps respectively but a 2-0 defeat in Belgium ended the Three Lions' hopes of reaching the UEFA Nations League final four.
In the same group, Gylfi Sigurdsson's Iceland were beaten 2-1 away against Jonas Lossl's Denmark.
Gareth Southgate named Pickford in his starting XI for England's crunch clash with the world's number one ranked nation and the Everton stopper could do little to keep out first-half efforts from Youri Tielemans and Dries Mertens that proved decisive.
Tielemans opened the scoring on 10 minutes with a 20-yard drive that took a nick off England's Tyrone Mings and careered in via the post, before Mertens bent a fine 23rd-minute free-kick into the top corner after Declan Rice was adjudged to have fouled Kevin de Bruyne.
Calvert-Lewin was introduced on 69 minutes with England chasing the game but couldn't add to the two international goals he has scored since making his senior debut against Wales last month. Everton defender Michael Keane was an unused substitute.
The loss in Leuven means England can no longer top Group A2 and, therefore, cannot qualify for the tournament's semi-finals as they did in 2019. The Three Lions will conclude their group fixtures against already-relegated Iceland at Wembley on Wednesday.
Sigurdsson was named captain in Copenhagen as he collected his 78th international cap.
Iceland, whose relegation to League B had already been confirmed before the latest round of fixtures, looked to have secured a point when Vidar Kjartansson netted five minutes from time to cancel out Christian Eriksen's first-half penalty.
However, Eriksen struck again from the penalty spot in injury-time to keep Danish hopes of progressing alive. Denmark - for whom Lossl was an unused substitute - will need to win away in Belgium on Wednesday to top the group ahead of their final match opponents.
Elsewhere, Joao Virginia did not feature but Portugal Under-21s defeated Cyprus 2-1 in their European Championship qualifier in Parchal.
Hungary's 1-1 draw with Serbia means Turkey could still secure promotion out of League B if they can win in Hungary on Wednesday and Russia fail to secure victory in Serbia.