Arsenal won 2-1 at the Santiago Bernabeu to complete a 5-1 aggregate victory and reach the semi-finals for the first time since 2009.
Madrid, led by superstars Kylian Mbappe and Vinicius Junior, largely failed to trouble Arsenal's defence until the latter struck in the 67th minute to level after Bukayo Saka's opener.
"We didn't have the accuracy up front, I don't think Raya had a save to make," Courtois told Movistar.
"We lost against a superior Arsenal and we have to accept it...
"We put in a lot of crosses but this year we don't have a Joselu, a born centre-forward up there, we have to analyse what we can do better."
Mbappe, who joined Madrid from PSG last summer, found it hard to escape Arsenal's defenders, who denied him the space he needs to thrive.
"I think we are a team, but we have to make more collective moves rather than individual ones," continued Courtois.
"If they double mark Vini or Kylian, a two-on-one might come off for you once, but not five times...
"It was very hard to generate danger... (Arsenal) are a team that is very hard to score against."