The woman, Isel Pineda, died before she was able to leave his office.
Dr. Oleg Davie, of Brooklyn, N.Y., is being charged with manslaughter and criminally negligent homicide.
Davie is alleged to have known about her heart transplant but in papers, he pretended he was not informed of it, noting that the large scar on her chest was from when a cyst was removed.
District Attorney Charles J. Hynes said doctors are discouraged from performing liposuction on patients with heart disease. Hynes said Davie was reckless in the procedure, falsifying the patient's medical history in paperwork.
She went into cardiac arrest in May 2012 while she was in his office. She died at Coney Island Hospital.
Pineda was a former model and received her heart transplant nearly 10 years before. The transplant surgery made it unsafe for her to be given general anesthesia.
Davie should not have performed any surgery on her, except for Botox or an invasive wart removal. He ignored her health history and performed "SmartLipo" on her.
Paperwork discovered in Pineda's purse by her boyfriend said Davie knew about the surgery because there were details about her diagnosis and the anti-rejection pills she took.
But when Davie filled out her patient history form, he marked "no" on the section that asks if she had ever been hospitalized.
He noted that she had a "mid-chest, old, well-healed" scar, that was from a "skin surgery to remove a cyst."
But Pineda's scar was much larger than that of a cyst, as it traveled form her neck all the way down to her navel.
Though she did not tell her family she was having liposuction, she did tell all of her friends and family about her heart transplant as it was something she was proud to survive.
"Anyone who met Isel knew she was a heart-transplant patient. She wore that label proudly, even posting it on her Facebook page," her family's lawyer Michael Fruhling said.
"That Dr. Davie failed to mention this is beyond comprehension."
She reportedly paid $3,200 for the lip, which is described in ads online as help to "lose the wobble."
Davie has been banned by the Health Department from a series of other procedures and a history of misconduct.
He has seven malpractice suits for negligence where he was fined $100,000 and put on probation for three years. Patients of his have complained about burns and disfigurement.