Ozil impressed in a three-year spell with Los Blancos, and has continued to shine at new club Arsenal following his £42.5 million switch on September 2.
"I was very surprised that Madrid let Ozil leave because he understands football better than any one else," Iniesta told Onda Cero.
"They will have had their reasons to let him go, though."
Iniesta then gave his thoughts on talk Real goalkeeper Iker Casillas or Pepe Reina could be roped in to replace Victor Valdes, who has confirmed he will leave Camp Nou when his contract expires at the end of the season.
"Valdes is the best and we will miss him a lot. He has made his decision, though," Iniesta lamented.
"[But] Casillas to Barcelona seems impossible to me. Reina? We would be delighted if he were to join Barca."
Iniesta also reiterated his desire to extend his stay with Barca, with his existing deal running until June 2015.
"My desire is to stay at Barcelona and the club want me to stay. There is not a problem if we both want the same thing."