Jones slammed his CBS sitcom in a taped testimonial for Forerunner Christian Church, calling Two and a Half Men "filth" and urging viewers to stop watching.
"If I am doing any harm, I don't want to be here. I don't want to be contributing to the enemy's plan... You cannot be a true God-fearing person and be on a television show like that," Jones said in the testimonial.
"I know I can't. I'm not okay with what I'm learning, what the Bible says and being on that television show."
His comments have now drawn a response from Supernatural's Padalecki, who chided Jones for accepting a reported $300,000 (£185,000) for each episode of the CBS series.
"AngusTJones -if you BELIEVE what you said, put ur money where ur mouth is and donate ur 'filthy' millions to charity. Try StJude ," Padalecki tweeted on Tuesday (November 27).
Jones has not issued any public comment on the controversy.
It was previously reported that work on Two and a Half Men is expected to commence as usual today.