The fatal strike fractured her skull behind the right ear and the shock caused such severe damage to her brain stem it killed her.
Callaghan earlier pleaded not guilty to the murder of Thomas, and was due to stand trial next February.
He also pleaded guilty to the charge of perverting the course of justice.
He has been remanded in custody until next March for a disputed facts hearing.
Outside court, Detective Inspector Mark Benefield, the public face of the murder inquiry, said investigators worked hard to solve the case.
"It was difficult. We had some real issues, especially around the media, that caused us hard work but it's a pleasing day for the family and members of the team who have got to this result.''
Police had empathy for the victims, he said.
"We have a five-year-old that's lost his father and mother. We have a mother that's lost her son. We have a mother that's lost her daughter. I'm a father and... prick me do I not bleed. I'm human."
Mr Benefield said he was proud of leading a team of dedicated staff who worked hard to resolve the case and which has resulted in today's plea.
"This has been an emotional investigation from the outset. The families on both sides have been ripped apart by violence and this development is particularly pertinent on White Ribbon Day where we all come together to express our intolerance of family violence."
New Zealand police attend about 240 family violence occurrences a day - one every six minutes - but police believe that reflects only about a fifth of all incidents as most go unreported.
Crown Solicitor Simon Moore SC, who has led the prosecution case, told media the guilty plea was very important for Ms Thomas family.
He said the guilty plea was helpful because it saved the community time and money of a trial but could not comment further because there was a sentencing process to go through.
"I think it is important that we don't say anything...until the sentence is passed.''
Callaghan's barrister Stuart Grieve QC said:
"Mr Callaghan is an intelligent young man who has taken responsibility for his actions in this tragic saga and has pleaded guilty to the two charges today which includes murder.''
He said it was a significant step for him to take but he had done so "responsibly''.
Callaghan and Ms Thomas had a young son together that they shared custody of. He is now being cared for by relatives.
