"It wasn't me," he said as the verdict was read in Brisbane Supreme Court on Tuesday.
The body of Ms Brooten, a 46-year-old American citizen living in Australia without a valid visa, has never been found.
Waden, 50, had been accused of killing her during an argument in July 2018 after she confronted him about seeing someone else.
The jury heard he buried her in a trench in his yard before disposing of her body at a rubbish tip almost a year later, launching an elaborate campaign of misdirection and deception to conceal her death.
"A jury has convicted you of the murder of a vibrant woman who was described as fully engaged with life," Justice Peter Callaghan said, handing down a life sentence minutes after the jury's verdict.
"The circumstances of her death cannot and apparently will not ever be known."
Not knowing the whereabouts of the body would be an ongoing trauma for Ms Brooten's daughter and all those who cared for the victim, Justice Callaghan said.
The prosecution alleged Waden killed Ms Brooten at the home they shared in Brisbane's north then made up stories about why she suddenly disappeared.
They included saying she left him for another man, was on the run from authorities or was living under an assumed identity.
Within weeks of Ms Brooten's disappearance, Waden invited his new love interest to his home and presented the missing woman's clothes, phone and make‑up as gifts.
In May 2019, there was a flurry of activity at the home after police visited, with the hiring of a self‑drive excavator and the purchase of tarpaulins and rope, along with trips to a rubbish tip.
"It is not known when or where exactly Mr Waden disposed of Ms Brooten's body," crown prosecutor Andrew Walklate told the jury.
"However, he may have disposed of her remains at the Nudgee dump."
The prosecution case was entirely circumstantial, built on phone tower data, car movements, Waden's alleged lies to friends, students and authorities, and the backyard excavation.
Defence barrister James Godbolt described it as "conjecture and speculation", arguing there was no body and no identified cause of death or forensic evidence tying Waden to murder.
Waden was being re-tried for the murder after his first trial was aborted earlier in June due to juror misconduct.
The jury handed down a murder verdict on its second day of deliberation.
Justice Callaghan told Waden the lack of a body and the extent of his deception would likely count against him when he sought release from prison.
Waden was sentenced to life with a mandatory minimum of 20 years before being eligible for parole.
His minimum sentence was reduced by 253 days due to time already served.
Waden did not visibly react as he handed his belongings to Corrective Services staff and was led from court to a holding cell.
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