More than 65,000 people signed a petition which stated the clip - featuring a pendant with the Arabic word for God on it being reduced to sand - was offensive, reported BBC online.
The music video has not been cut, but the pendant has now been digitally "scrubbed" out of the scene.
Petition instigator Shazad Iqbal, said he was "thrilled" with the outcome.
"The name of Allah has been removed from the Dark Horse video - we couldn't have done it without everyone's support so I thank each and every one of you deeply, our voices have been heard," he wrote on Change.Org.
It is unclear whether YouTube made the change or if it was instructed to by Perry's record company.