Fellaini was ruled out of the Cardiff clash with a groin strain after scoring twice in Belgium’s stunning 4-3 friendly victory over France in Paris on Sunday night.
The Manchester United midfielder had a strong finish to the Premier League season and Wales manager Chris Coleman had spoken about the big Belgian’s power and aerial ability ahead of the Group B clash.
“Fellaini is really important for us. He showed that against France,” said Chelsea star Courtois. “Marouane is physically strong and Wales have a few strong players, so it would have helped to have him in the team.
“But we have a team with a lot of qualities and another player will come in for him and do the best he can.”
Belgium top the group at the halfway stage of the campaign but only on goal difference from a Wales side who are also unbeaten after five games.
Top-seeds Bosnia-Herzegovina have six points to make up on the top two in the second half of the campaign and Courtois feels Wales have now emerged as the biggest threat to Belgium.
The top two will automatically qualify for the European Championships in France next summer, with the third-placed team guaranteed at least a play-off spot.
“When you saw the draw at the start, the three teams that were the hardest were Belgium, Wales and Bosnia,” Courtois said.
“Wales are now closest to us with Bosnia a bit behind us, so I think at this moment they are the biggest threat and we have to try to win the game.
“There are still five games to go so a lot can happen but whoever wins this game will be a step closer going to France.
“It is not a surprise Wales are there because a lot of their players play in England and they have a good team.”
Gareth Bale will be the greatest danger to Courtois keeping a clean sheet at the Cardiff City Stadium and the Welshman memorably scored past the Belgian in the 2014 Champions League final between Real Madrid and Atletico.
But Courtois dismissed the idea of getting his own back on Bale for that goal, saying: “I don’t need revenge.
“Bale is a great player and he has scored some important goals for Real Madrid. Maybe he is their biggest player but Wales have a very good team that know how to put a block together.
“They know how to defend well and not give us chances, and if we do get a chance we have to score.
“I think they will look to counter-attack and really hurt the space at the back – so we have to defend well too.”
Watch Wales v Belgium live on Sky Sports 5 HD from 7pm on Friday.