The film for his new single Tarzan 2 originally had the message “Free Leo Chindamo” in the opening credits.
Chindamo was jailed last year after breaching the terms of his licence by meeting a gang member, breaking a curfew and failing a breath test, it is understood.
He was originally jailed for life with a minimum of 12 years after stabbing Mr Lawrence outside his school in west London.
A spokesman for the star said the film, which had more than 225,000 views on YouTube since it was posted on 3 July, had been taken down and will be re-edited without the reference to Chindamo.
He added that Dappy would donate all his “personal royalties” from the track to crime reduction charity Nacro.
Yesterday, Dappy apologised and said he “honestly wasn’t aware” of the high-profile crime which shocked Britain in December 1995.
He wrote: “I knew his brother from when I was young.
“In no way did I intend to cause upset and certainly didn’t know about his past.
“My heart goes out to Mr Lawrence’s family.
“I know too well the pain of losing a loved one, sincerely Dappy.”
The video also sees the rapper have a pop at Simon Cowell and X Factor stars.