The 52-year-old actor has denied any wrongdoing.
Haim, 38, died in 2010 of pneumonia after years of substance abuse. His mother Judy has repeatedly said there was no inappropriate or violent relationship between her son and Sheen.
Named as defendants in Sheen's lawsuit -- along with the National Enquirer -- are the tabloid's editor-in-chief Dylan Howard and actor Dominick Brascia, who was the source for the story, ETOnline said.
Sheen is asking for unlimited monetary and punitive damages, recovery of his legal team's fees and a jury trial to resolve the case.
The actor's representatives said in court papers Howard published the story about Sheen "because of a personal vendetta that arose after he was unable to be the first to break the story that Mr. Sheen was HIV positive."
"In my nearly 35 years as a celebrated entertainer, I have been nothing shy of a forthright, noble and valiant courier of the truth. Consistently admitting and owning a laundry list of shortcomings, wrongdoings and indiscretions this traveler hath traveled -- however, every man has a breaking point," Sheen told TMZ. "These radically groundless and unfounded allegations end now. I now take a passionate stand against those who wish to even entertain the sick and twisted lies against me. Game Over."