The Belgian club's European journey was cut short after a 4-1 aggregate defeat in the second leg in Spain.
Onyedika, a key figure in their midfield, was forced to miss the crucial second leg after accumulating yellow cards for the campaign in the first match at home.
Hugo Vetlesen was brought in to replace Onyedika, and while Degryse acknowledged his effort, he noted the player's lack of match sharpness was apparent.
What Degryse said about Onyedika
After the game, Degryse argued that the Nigerian international's absence dealt a significant blow to Club Brugge's tactical setup, forcing coach Ivan Leko into a major reshuffle for the decisive away fixture.
Speaking to Het Laatste Nieuws, Degryse explained, "Ivan Leko’s choice of Vetlesen was certainly a good one.
“He was often in the right place and offered himself. Excellent. You just felt he lacked rhythm and feeling."
He suggested that with Onyedika on the pitch, the team's dynamics would have been entirely different, potentially leading to a better outcome.
"If you play the second leg against Atlético with Onyedika, Stankovic will be in the spaces where Vetlesen was now," Degryse added. "Had Stankovic had those chances, he would certainly have scored once or twice."
Following their European exit, Club Brugge will now turn their attention to domestic competitions, left to reflect on a campaign that highlighted areas for improvement ahead of future continental challenges.