The Brisbane Supreme Court jury of six men and six women returned the unanimous verdict shortly after 1pm on Thursday, after seven-and-a-half hours of deliberations.
Daniel, 13, vanished while waiting for a bus at Woombye on the Sunshine Coast on December 7, 2003.
His remains were found in bushland in the Sunshine Coast hinterland in 2011.
Denise Morcombe called Cowan a "perverted soul" who didn't realise she "would never give up searching for answers" during a victim impact statement read by Crown prosecutor Michael Byrne QC during Cowan's sentence.
"That was your mistake, you evil, evil, unhuman thing," she wrote.
Ms Morcombe still had nightmares and was haunted by images of her son lying in "dark eerie bushland being destroyed by wild animals".
"I made a vow to Daniel I would find out where he is and justice will be done," she said.
"I have lived and breathed each day to find the answers."
She said Mr Cowan was a "sexual freak" who had no respect for human life.
"This day hasn't brought closure, but the streets are safer without you walking them and looking for your next target to destroy."
Her and her husband's victim impact statements spoke of how the former truck driver had destroyed their family.
Mr Morcombe said Cowan had been exposed as an "opportunistic, perverted, cold-blooded child-killing pedophile" in his statement, which he read from the witness box.
Their words were applauded by the packed public gallery, which included family members, police officers and members of the public.
Daniel's twin Bradley and older brother Dean described how the horrendous crime had ruined their family.
Dean said Cowan's attempt at molesting his brother was "sickening", but his complete lack of remorse for killing Daniel was even worse.
Bradley's statement, read out by Mr Byrne, said he'd wanted to be a pilot but all his dreams had fallen apart following Daniel's abduction.
Mr Byrne said Cowan should be jailed without parole for longer than the mandatory minimum of 15 years.
Cowan had "numerous and on occasions highly relevant" prior convictions, including two for raping boys aged six and seven, for which he was sentenced to a total of nine years in jail.
Cowan's defence barrister Angus Edwards argued for leniency, saying his client didn't intentionally kill Daniel.
Justice Roslyn Atkinson paid tribute to the Morcombe family's strength and the way they conducted themselves and recognised the "stunning" work by covert police officers to arrest Cowan.
Outside court, Queensland's assistant police commissioner Mike Condon said police were happy a guilty verdict had been delivered.
Child protection advocate Bravehearts founder Hetty Johnstone commended the Morcombes, but said they had been badly let down by inadequate sex offender laws.
"Daniel didn't have to die, he should be here today if the system got it right," she said.
Outside court, Mr and Mrs Morcombe thanked those involved for "never forgetting Daniel".
Cowan's trial lasted four-and-a-half weeks and heard evidence from 116 witnesses.
He was arrested on August 13, 2011 and has been in custody since then.
His sentence was adjourned.
- AAP
