The decision was reportedly made because discussions surrounding the similarity were overshadowing the central figure of the film, Jesus.
"It gives me great pleasure to tell you that the devil is on the cutting room floor," said Roma Downey, one of the film's producers, according to the Guardian.
"For our movie, Son of God, I wanted all the focus to be on Jesus. I want his name to be on the lips of everyone who sees this movie, so we cast Satan out.
"I was sure everyone would only be talking about Jesus, but they were talking about Satan instead."
The film is made from the material in the hit TV miniseries "The Bible".
The resemblance between actor Mohamen Mehdi Ouazanni and the American Commander in Chief was first noted in March 2013 when the series was first broadcast in the US.
At that time, the producers released the following statement quoted in the Independent. "[Mr Ouzanni] has previously played parts in several Biblical epics - including satanic characters - long before Barack Obama was elected as our president.
"We have nothing but respect and love for our president, who is a fellow Christian."
Speaking against suggestions that they made the casting choice because of the resemblance, they said "False statements such as these are just designed as a foolish distraction to try and discredit the beauty of the story of The Bible."
The original ten-hour run of "The Bible" attracted 13.1 million viewers for its premier when it was broadcast in the UK last November, beating American Idol.
20th Century Fox releases Son of God on Friday 28 February.