Belgium was knocked out of the World Cup at the group stage while Croatia advanced at their expense with a goalless draw in Qatar.
Roberto Martinez’s side, who finished third in Russia four years ago, as well as ranked second in the world, have had a disappointing tournament with just one win in three matches.
They put in another lackluster display against Croatia despite knowing a win was necessary to progress to the last 16.
Substitute Romelu Lukaku had numerous chances in the second half but failed to convert any.
Lukaku, still returning to full fitness following injury, poked an effort wide and then reacted too late when the ball hit him in front of the goal in stoppage time.
Croatia, finalists in 2018, got the point they needed to progress from Group F as runners-up, with Morocco taking the top spot following a 2-1 win against Canada.
Zlatko Dalic’s side will face the winners of Group E – which is currently Spain – in the last 16.