The 33-year-old paedophile has also been found guilty of sexually and physically abusing the 15-month-old toddler.
The jury at Dungannon Crown Court found Millie's 28-year-old mother, Rachael Martin "not guilty" of involvement in her daughter's death.
The judge, Mr. Justice Stephens, told McCarney that his "despicable crime is almost beyond understanding" as he passed the mandatory life sentence, and put him on the Sex Offender's Register.
Mr. Justice Stephens also told McCarney that "this jury has clearly understood, and you for your part should understand, you are going to prison for a very long period of time".
McCarney, of Woodview Crescent, Trillick, displayed no emotion at his conviction, which comes just a week shy of the anniversary of Millie's death on December 11, 2009, from massive head injuries.
However, Millie's mother, Rachael, who turned 28 last week, wept uncontrollably in the dock, as she was acquitted of involvement in the death of her 15-month-old toddler. Hugging her sides and swaying backwards and forwards in the dock, she repeated over and over..."thank-you, oh thank- you", before adding "justice has been done for my daughter".
Martin of Main Street, Kesh, who maintained she'd done everything to protect her "angel" was cleared of allowing McCarney to kill her daughter and of wilfully neglecting her during the three months she and him were lovers.
It had taken the jury just under three hours to reach their unanimous verdicts which were greeted with muted cheers and air-punches by family and friends of Martin in the packed public gallery.
Mr. Justice Stephens, while jailing McCarney for life for murder, will hold a tariff hearing in the New Year to determine how long the convicted killer will have to serve before it is considered safe for him to be released back into society.
During the 10-week trial the court heard that in addition to the fatal blow to the back of her head, Millie had suffered a multitude of other injuries, including horrific internal injuries which could have proved just as fatal.
These injuries to her abdomen had been caused by punching or prodding not only in the weeks, but possibly even in the hours before her death.
The child also had 21 cracked ribs. According to specialists seven were old and healing, while a further 14 were less than 10 days old and still fresh. These wounds, it was said, had been caused by grabbing and forcibly squeezing the child's small chest.
There were also multiple bruises, almost from head to toe on her infant body, and an oval, egg-shaped lump on her forehead, which was clearly visible for all to see in the weeks leading to her murder.
Millie had also been subjected to a sexual assault, which it was suggested may have been caused by blunt force trauma, such as a punch to her genital area, as opposed to actual penetration.
Throughout the 35 days of evidence and legal argument, McCarney never once spoke in his own behalf, instead he relied on his defence QC Eilis McDermott to cross-examine witnesses and to make his case that he was the innocent victim of vile circumstance.
By their verdict the jury have rejected Ms McDermott's claims it was his lover, the child's mother, who was really the guilty party, and that the only evidence against McCarney was the word of the investigating police, backed by the prosecution.
The lawyer had claimed that McCarney was an innocent, unaware that Millie's mother: "didn't want the doctor, the social services involved, not because Mr. McCarney was doing these terrible things with her permission, but that she was doing these things herself."
The jury also appears to have refuted Ms McDermott assertion that there was "zero" for them to consider for while the "police say it was him, the prosecution say it was him", there was "not a scrap of forensic evidence" against McCarney, even though "no stone had been left unturned".
Instead the jury accepted the case of prosecution QC Ciaran Murphy who successfully argued that Millie was the victim of "vile, sadistic abuse" and that as a jury, because "Millie's life was short, sad and cruel", they should, "do justice for her".
They must also have accpeted an adverse inference could be taken against McCarney in his refusal to give evidence on his own behalf, in a case which the prosecution claimed had cried "out for explanation .... instead he has chosen silence".
However, the jury, by their verdicts, rejected the prosecution case that Millie's mother was equally guilty for having "turned a blind eye" to McCarney's abuse.
Mr. Murphy had argued that she did not need hindsight to understand what Millie was suffering, all she needed was to "open her eyes and see what was going on in her own house with her own daughter".
The jury thought otherwise, deciding that Martin had done everything a mother could do to protect her baby daughter, unaware, as she herself had said, that she had unwittingly let a "monster" into her home.
They also accepted the assertion of her defence QC John McCrudden that nothing could be further from the truth that Martin had turned from being a loving, caring, devoted mother into a vile, evil murderess.